biocontainers/samtools:v1.7.0_cv4 centos:centos6 quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1
using singularity
+ set -o pipefail
+ '[' input_3 = '' ']'
++ head -n 1
++ ls -LS input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.amb input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.ann input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.bwt input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.pac input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.sa
++ grep '[.]bwt$'
++ sed 's/.bwt$//'
+ ref=input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa
+ mkdir -p output.bwa
+ xargs -I '{}' -P 1 bash -c '{}'
++ find input_1/
++ egrep '(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'
+ for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`'
++ echo input_1/SRR4425244_1.fastq
++ egrep '_1[.]f(ast|)q(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425244_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ i2=input_1/SRR4425244_2.fastq
++ basename input_1/SRR4425244_1.fastq
++ sed 's/_1[.]f.*//'
++ sed 's/_R1.*//'
+ outbase=output.bwa/SRR4425244
++ basename input_1/SRR4425244_1.fastq
++ sed 's/_1[.]f.*//'
++ sed 's/_R1.*//'
+ samplename=SRR4425244
+ echo 'singularity exec -B /suikou/files/m64g/user2/work/yoshitake/117:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1  bwa mem  -t 8 -R \'\''@RG\\tID:SRR4425244\\tSM:SRR4425244\\tLB:library\'\'' \'\''input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa\'\'' \'\''input_1/SRR4425244_1.fastq\'\'' \'\''input_1/SRR4425244_2.fastq\'\'' | singularity exec -B /suikou/files/m64g/user2/work/yoshitake/117:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4  samtools sort -@ 8 -o \'\''output.bwa/SRR4425244\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/yoshitake/117:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4  samtools index \'\''output.bwa/SRR4425244\'\''.bam'
+ for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`'
++ echo input_1/SRR4425245_1.fastq
++ egrep '_1[.]f(ast|)q(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425245_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ i2=input_1/SRR4425245_2.fastq
++ basename input_1/SRR4425245_1.fastq
++ sed 's/_1[.]f.*//'
++ sed 's/_R1.*//'
+ outbase=output.bwa/SRR4425245
++ basename input_1/SRR4425245_1.fastq
++ sed 's/_1[.]f.*//'
++ sed 's/_R1.*//'
+ samplename=SRR4425245
+ echo 'singularity exec -B /suikou/files/m64g/user2/work/yoshitake/117:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1  bwa mem  -t 8 -R \'\''@RG\\tID:SRR4425245\\tSM:SRR4425245\\tLB:library\'\'' \'\''input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa\'\'' \'\''input_1/SRR4425245_1.fastq\'\'' \'\''input_1/SRR4425245_2.fastq\'\'' | singularity exec -B /suikou/files/m64g/user2/work/yoshitake/117:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4  samtools sort -@ 8 -o \'\''output.bwa/SRR4425245\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/yoshitake/117:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4  samtools index \'\''output.bwa/SRR4425245\'\''.bam'
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 200000 sequences (20200000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (75, 89047, 22, 110)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (43, 86, 297)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 805)
[M::mem_pestat] mean and std.dev: (111.78, 115.69)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1059)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (141, 207, 497)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1209)
[M::mem_pestat] mean and std.dev: (286.01, 247.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1565)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (110, 455, 901)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2483)
[M::mem_pestat] mean and std.dev: (410.10, 368.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3274)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (53, 151, 703)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2003)
[M::mem_pestat] mean and std.dev: (312.16, 443.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2653)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 200000 reads in 20.749 CPU sec, 2.635 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 8 -R @RG\tID:SRR4425244\tSM:SRR4425244\tLB:library input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa input_1/SRR4425244_1.fastq input_1/SRR4425244_2.fastq
[main] Real time: 3.808 sec; CPU: 21.383 sec
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 200000 sequences (20000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (89, 87150, 26, 98)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (42, 86, 191)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 489)
[M::mem_pestat] mean and std.dev: (103.32, 95.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 638)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (142, 211, 482)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1162)
[M::mem_pestat] mean and std.dev: (277.82, 228.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1502)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (89, 355, 1207)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3443)
[M::mem_pestat] mean and std.dev: (645.83, 753.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4561)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (74, 180, 761)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2135)
[M::mem_pestat] mean and std.dev: (403.90, 523.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2822)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 200000 reads in 23.807 CPU sec, 3.018 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 8 -R @RG\tID:SRR4425245\tSM:SRR4425245\tLB:library input_3/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa input_1/SRR4425245_1.fastq input_1/SRR4425245_2.fastq
[main] Real time: 3.949 sec; CPU: 24.410 sec
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'singularity exec -B /suikou/files/m64g/user2/work/yoshitake/117:/mnt --pwd /mnt /home/user2/img/' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ echo 0
+ exit