centos:centos6 quay.io/biocontainers/fastqc:0.11.8--1 quay.io/biocontainers/sickle-trim:1.33--ha92aebf_4
using docker
+ set -o pipefail
++ find input_1/
++ egrep '[.]f(ast|)q$'
+ cat input_1/out-20171105_1126_171105_Loman_Ecoli.fastq
+ docker run -v /data/user2/work/83:/data/user2/work/83 -w /data/user2/work/83 -u root -i --rm quay.io/biocontainers/fastqc:0.11.8--1 fastqc -t 8 --extract input.fastq
Started analysis of input.fastq
Approx 5% complete for input.fastq
Approx 10% complete for input.fastq
Approx 20% complete for input.fastq
Approx 35% complete for input.fastq
Approx 45% complete for input.fastq
Approx 55% complete for input.fastq
Approx 70% complete for input.fastq
Approx 80% complete for input.fastq
Approx 95% complete for input.fastq
Analysis complete for input.fastq
+ rm -f input.fastq
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1/
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"`'
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/sickle-trim:1.33--ha92aebf_4 sickle se -f input_1/out-20171105_1126_171105_Loman_Ecoli.fastq -o input_1/out-20171105_1126_171105_Loman_Ecoli.fastq.sickle -t sanger -q 15 -l 5000

FastQ records kept: 3379
FastQ records discarded: 5970

+ cat input_1/out-20171105_1126_171105_Loman_Ecoli.fastq.sickle
+ docker run -v /data/user2/work/83:/data/user2/work/83 -w /data/user2/work/83 -u root -i --rm quay.io/biocontainers/fastqc:0.11.8--1 fastqc -t 8 --extract output.sickle.fastq
Started analysis of output.sickle.fastq
Approx 20% complete for output.sickle.fastq
Approx 55% complete for output.sickle.fastq
Approx 85% complete for output.sickle.fastq
Analysis complete for output.sickle.fastq
+ rm -f input_1/out-20171105_1126_171105_Loman_Ecoli.fastq.sickle
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ docker run -v /data/user2/work/83:/data/user2/work/83 -w /data/user2/work/83 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit