script: mapping-illumina~HISAT2 "$scriptdir"/convert~gff3_to_gtf
c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6 quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3
using docker
+ set -o pipefail
+ '[' input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fainput_4 = '' ']'
++ find input_1/
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
+ r1='input_1/SRR4425244_1.fastq
input_1/SRR4425245_1.fastq
input_1/SRR4425248_1.fastq
input_1/SRR4425249_1.fastq
input_1/SRR4425250_1.fastq
input_1/SRR4425251_1.fastq'
++ find input_1/
++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$'
++ echo ''
+ r1gz=
+ '[' 'input_1/SRR4425244_1.fastq
input_1/SRR4425245_1.fastq
input_1/SRR4425248_1.fastq
input_1/SRR4425249_1.fastq
input_1/SRR4425250_1.fastq
input_1/SRR4425251_1.fastq' = '' ']'
++ for i in '$r1'
+++ echo input_1/SRR4425244_1.fastq
+++ egrep '_1[.]f(ast|)q$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1/SRR4425244_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
++ for i in '$r1'
+++ echo input_1/SRR4425245_1.fastq
+++ egrep '_1[.]f(ast|)q$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1/SRR4425245_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
++ for i in '$r1'
+++ echo input_1/SRR4425248_1.fastq
+++ egrep '_1[.]f(ast|)q$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1/SRR4425248_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
++ for i in '$r1'
+++ echo input_1/SRR4425249_1.fastq
+++ egrep '_1[.]f(ast|)q$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1/SRR4425249_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
++ for i in '$r1'
+++ echo input_1/SRR4425250_1.fastq
+++ egrep '_1[.]f(ast|)q$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1/SRR4425250_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
++ for i in '$r1'
+++ echo input_1/SRR4425251_1.fastq
+++ egrep '_1[.]f(ast|)q$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1/SRR4425251_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ r2='input_1/SRR4425244_2.fastq
input_1/SRR4425245_2.fastq
input_1/SRR4425248_2.fastq
input_1/SRR4425249_2.fastq
input_1/SRR4425250_2.fastq
input_1/SRR4425251_2.fastq'
+ r2gz=
+ echo '#Check paired-end'
#Check paired-end
+ ls input_1/SRR4425244_2.fastq input_1/SRR4425245_2.fastq input_1/SRR4425248_2.fastq input_1/SRR4425249_2.fastq input_1/SRR4425250_2.fastq input_1/SRR4425251_2.fastq
++ echo input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ egrep '[.](gff|gff3)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ sed 's/[.]\(gff\|gff3\)$/.gtf/'
+ temp_3=input_3/Bomo_gene_models.withnote.plus.NC_002355.gtf
+ bash /data/user2/work/69/convert~gff3_to_gtf input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6 quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3
using docker
+ set -o pipefail
++ echo input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ awk '-F\t' '{OFS="\t"; gsub(/%../,"_",$9); gsub(/[^0-9a-zA-Z_;=-]/,"_",$9); print $0}' input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
+ awk '-F\t' '{
  split($9,arr,";"); str=""; for(i=1;i<=length(arr);i++){if(arr[i]!~"^[_0-9]"){if(str==""){str=arr[i]}else{str=str";"arr[i]}}};
  $9=str; OFS="\t"; print $0
 }'
+ awk '{
  if($0!~"^#"){
   OFS="\t"; split($9,arr,";"); str="";
   for(i=1;i<=length(arr);i++){
    if(arr[i]~"^ID=" || arr[i]~"^Name=" || arr[i]~"^Note=" || arr[i]~"^Parent"){
     if(str==""){str=arr[i]}else{str=str";"arr[i]}
    }else{
     if(str==""){str=tolower(substr(arr[i],1,1))""substr(arr[i],2)}else{str=str";"tolower(substr(arr[i],1,1))""substr(arr[i],2)}
    }
   };
   $9=str
  };
  print $0
 }'
++ echo input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ sed 's/[.]\(gff\|gff3\)$/.gtf/'
+ temp_1=input_3/Bomo_gene_models.withnote.plus.NC_002355.gtf
++ echo input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ sed 's/[.]\(gff\|gff3\)$/.withname.gtf/'
+ temp_2=input_3/Bomo_gene_models.withnote.plus.NC_002355.withname.gtf
+ docker run -v /data/user2/work/69:/data/user2/work/69 -w /data/user2/work/69 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 gff3ToGenePred input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3.rename /dev/stdout
+ docker run -v /data/user2/work/69:/data/user2/work/69 -w /data/user2/work/69 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 genePredToGtf file stdin input_3/Bomo_gene_models.withnote.plus.NC_002355.gtf
+ sed 's/ \+/ /g' input_3/Bomo_gene_models.withnote.plus.NC_002355.gtf
+ awk '-F\t' '
 FILENAME==ARGV[1] && $3=="gene"{
  split($9,arr,";"); id=""; name=""; note=""; for(i in arr){
   if(tolower(substr(arr[i],1,3))=="id="){id=substr(arr[i],4)}
   else if(tolower(substr(arr[i],1,5))=="gene="){name=substr(arr[i],6)}
   else if(tolower(substr(arr[i],1,5))=="note="){note=substr(arr[i],6)}};
  if(id!="" && name!="" && note!=""){id2name[id]=name"_"note}
  else if(id!="" && name!="" && note==""){id2name[id]=name}
  else if(id!="" && name=="" && note!=""){id2name[id]=note}
 }
 FILENAME==ARGV[2]{
  a=$0; sub(/.*; gene_name "/,"",a); sub(/".*/,"",a);
  if(a!~"\t" && id2name[a]!=""){b=$0; c=$0; sub(/; gene_name ".*/,"; gene_name \"",b); sub(/.*; gene_name "[^"]*"/,"\"",c); print b""id2name[a]""c}else{print $0}
 }' input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3.rename /dev/stdin
+ post_processing
+ '[' 2 = 1 ']'
+ exit
+ input_3=input_3/Bomo_gene_models.withnote.plus.NC_002355.gtf
+ '[' input_4 = '' ']'
++ ls input_4/hisat2_index.1.ht2
++ sed 's/.1.ht2$//'
+ index=input_4/hisat2_index
+ mkdir -p output.prinseq
+ for i in '$r1'
+ xargs -I '{}' -P 8 bash -c '{}'
++ echo input_1/SRR4425244_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425244_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=input_1/SRR4425244_2.fastq
++ basename input_1/SRR4425244_1.fastq
+ i2=SRR4425244_1.fastq
++ basename input_1/SRR4425244_2.fastq
+ j2=SRR4425244_2.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 prinseq-lite.pl -fastq input_1/SRR4425244_1.fastq -fastq2 input_1/SRR4425244_2.fastq -out_good output.prinseq/SRR4425244_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/SRR4425244_1.fastq_1.fastq 'output.prinseq/SRR4425244_1.fastq;' mv output.prinseq/SRR4425244_1.fastq_2.fastq output.prinseq/SRR4425244_2.fastq
+ for i in '$r1'
++ echo input_1/SRR4425245_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425245_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=input_1/SRR4425245_2.fastq
++ basename input_1/SRR4425245_1.fastq
+ i2=SRR4425245_1.fastq
++ basename input_1/SRR4425245_2.fastq
+ j2=SRR4425245_2.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 prinseq-lite.pl -fastq input_1/SRR4425245_1.fastq -fastq2 input_1/SRR4425245_2.fastq -out_good output.prinseq/SRR4425245_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/SRR4425245_1.fastq_1.fastq 'output.prinseq/SRR4425245_1.fastq;' mv output.prinseq/SRR4425245_1.fastq_2.fastq output.prinseq/SRR4425245_2.fastq
+ for i in '$r1'
++ echo input_1/SRR4425248_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425248_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=input_1/SRR4425248_2.fastq
++ basename input_1/SRR4425248_1.fastq
+ i2=SRR4425248_1.fastq
++ basename input_1/SRR4425248_2.fastq
+ j2=SRR4425248_2.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 prinseq-lite.pl -fastq input_1/SRR4425248_1.fastq -fastq2 input_1/SRR4425248_2.fastq -out_good output.prinseq/SRR4425248_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/SRR4425248_1.fastq_1.fastq 'output.prinseq/SRR4425248_1.fastq;' mv output.prinseq/SRR4425248_1.fastq_2.fastq output.prinseq/SRR4425248_2.fastq
+ for i in '$r1'
++ echo input_1/SRR4425249_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425249_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=input_1/SRR4425249_2.fastq
++ basename input_1/SRR4425249_1.fastq
+ i2=SRR4425249_1.fastq
++ basename input_1/SRR4425249_2.fastq
+ j2=SRR4425249_2.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 prinseq-lite.pl -fastq input_1/SRR4425249_1.fastq -fastq2 input_1/SRR4425249_2.fastq -out_good output.prinseq/SRR4425249_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/SRR4425249_1.fastq_1.fastq 'output.prinseq/SRR4425249_1.fastq;' mv output.prinseq/SRR4425249_1.fastq_2.fastq output.prinseq/SRR4425249_2.fastq
+ for i in '$r1'
++ echo input_1/SRR4425250_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425250_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=input_1/SRR4425250_2.fastq
++ basename input_1/SRR4425250_1.fastq
+ i2=SRR4425250_1.fastq
++ basename input_1/SRR4425250_2.fastq
+ j2=SRR4425250_2.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 prinseq-lite.pl -fastq input_1/SRR4425250_1.fastq -fastq2 input_1/SRR4425250_2.fastq -out_good output.prinseq/SRR4425250_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/SRR4425250_1.fastq_1.fastq 'output.prinseq/SRR4425250_1.fastq;' mv output.prinseq/SRR4425250_1.fastq_2.fastq output.prinseq/SRR4425250_2.fastq
+ for i in '$r1'
++ echo input_1/SRR4425251_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/SRR4425251_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=input_1/SRR4425251_2.fastq
++ basename input_1/SRR4425251_1.fastq
+ i2=SRR4425251_1.fastq
++ basename input_1/SRR4425251_2.fastq
+ j2=SRR4425251_2.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 prinseq-lite.pl -fastq input_1/SRR4425251_1.fastq -fastq2 input_1/SRR4425251_2.fastq -out_good output.prinseq/SRR4425251_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/SRR4425251_1.fastq_1.fastq 'output.prinseq/SRR4425251_1.fastq;' mv output.prinseq/SRR4425251_1.fastq_2.fastq output.prinseq/SRR4425251_2.fastq
Input and filter stats:
	Input sequences (file 1): 100,000
	Input bases (file 1): 10,100,000
	Input mean length (file 1): 101.00
	Input sequences (file 2): 100,000
	Input bases (file 2): 10,100,000
	Input mean length (file 2): 101.00
	Good sequences (pairs): 98,443
	Good bases (pairs): 19,885,486
	Good mean length (pairs): 202.00
	Good sequences (singletons file 1): 924 (0.92%)
	Good bases (singletons file 1): 93,324
	Good mean length (singletons file 1): 101.00
	Good sequences (singletons file 2): 243 (0.24%)
	Good bases (singletons file 2): 24,543
	Good mean length (singletons file 2): 101.00
	Bad sequences (file 1): 633 (0.63%)
	Bad bases (file 1): 63,933
	Bad mean length (file 1): 101.00
	Bad sequences (file 2): 924 (0.92%)
	Bad bases (file 2): 93,324
	Bad mean length (file 2): 101.00
	Sequences filtered by specified parameters:
	trim_qual_right: 294
	trim_tail_right: 14
	min_len: 975
	ns_max_p: 664
Input and filter stats:
	Input sequences (file 1): 100,000
	Input bases (file 1): 10,100,000
	Input mean length (file 1): 101.00
	Input sequences (file 2): 100,000
	Input bases (file 2): 10,100,000
	Input mean length (file 2): 101.00
	Good sequences (pairs): 97,935
	Good bases (pairs): 19,782,870
	Good mean length (pairs): 202.00
	Good sequences (singletons file 1): 1,044 (1.04%)
	Good bases (singletons file 1): 105,444
	Good mean length (singletons file 1): 101.00
	Good sequences (singletons file 2): 251 (0.25%)
	Good bases (singletons file 2): 25,351
	Good mean length (singletons file 2): 101.00
	Bad sequences (file 1): 1,021 (1.02%)
	Bad bases (file 1): 103,121
	Bad mean length (file 1): 101.00
	Bad sequences (file 2): 1,044 (1.04%)
	Bad bases (file 2): 105,444
	Bad mean length (file 2): 101.00
	Sequences filtered by specified parameters:
	trim_qual_right: 573
	trim_tail_right: 11
	min_len: 1049
	ns_max_p: 1202
Input and filter stats:
	Input sequences (file 1): 100,000
	Input bases (file 1): 10,100,000
	Input mean length (file 1): 101.00
	Input sequences (file 2): 100,000
	Input bases (file 2): 10,100,000
	Input mean length (file 2): 101.00
	Good sequences (pairs): 98,286
	Good bases (pairs): 19,853,772
	Good mean length (pairs): 202.00
	Good sequences (singletons file 1): 1,013 (1.01%)
	Good bases (singletons file 1): 102,313
	Good mean length (singletons file 1): 101.00
	Good sequences (singletons file 2): 325 (0.33%)
	Good bases (singletons file 2): 32,825
	Good mean length (singletons file 2): 101.00
	Bad sequences (file 1): 701 (0.70%)
	Bad bases (file 1): 70,801
	Bad mean length (file 1): 101.00
	Bad sequences (file 2): 1,013 (1.01%)
	Bad bases (file 2): 102,313
	Bad mean length (file 2): 101.00
	Sequences filtered by specified parameters:
	trim_qual_right: 244
	trim_tail_right: 14
	min_len: 1122
	ns_max_p: 710
Input and filter stats:
	Input sequences (file 1): 100,000
	Input bases (file 1): 10,000,000
	Input mean length (file 1): 100.00
	Input sequences (file 2): 100,000
	Input bases (file 2): 10,000,000
	Input mean length (file 2): 100.00
	Good sequences (pairs): 97,729
	Good bases (pairs): 19,545,800
	Good mean length (pairs): 200.00
	Good sequences (singletons file 1): 1,579 (1.58%)
	Good bases (singletons file 1): 157,900
	Good mean length (singletons file 1): 100.00
	Good sequences (singletons file 2): 378 (0.38%)
	Good bases (singletons file 2): 37,800
	Good mean length (singletons file 2): 100.00
	Bad sequences (file 1): 692 (0.69%)
	Bad bases (file 1): 69,200
	Bad mean length (file 1): 100.00
	Bad sequences (file 2): 1,579 (1.58%)
	Bad bases (file 2): 157,900
	Bad mean length (file 2): 100.00
	Sequences filtered by specified parameters:
	trim_qual_right: 657
	trim_tail_right: 16
	min_len: 1409
	ns_max_p: 503
Input and filter stats:
	Input sequences (file 1): 100,000
	Input bases (file 1): 10,000,000
	Input mean length (file 1): 100.00
	Input sequences (file 2): 100,000
	Input bases (file 2): 10,000,000
	Input mean length (file 2): 100.00
	Good sequences (pairs): 97,562
	Good bases (pairs): 19,512,400
	Good mean length (pairs): 200.00
	Good sequences (singletons file 1): 329 (0.33%)
	Good bases (singletons file 1): 32,900
	Good mean length (singletons file 1): 100.00
	Good sequences (singletons file 2): 1,627 (1.63%)
	Good bases (singletons file 2): 162,700
	Good mean length (singletons file 2): 100.00
	Bad sequences (file 1): 2,109 (2.11%)
	Bad bases (file 1): 210,900
	Bad mean length (file 1): 100.00
	Bad sequences (file 2): 329 (0.33%)
	Bad bases (file 2): 32,900
	Bad mean length (file 2): 100.00
	Sequences filtered by specified parameters:
	trim_qual_right: 815
	trim_tail_right: 12
	min_len: 1395
	ns_max_p: 698
Input and filter stats:
	Input sequences (file 1): 100,000
	Input bases (file 1): 10,100,000
	Input mean length (file 1): 101.00
	Input sequences (file 2): 100,000
	Input bases (file 2): 10,100,000
	Input mean length (file 2): 101.00
	Good sequences (pairs): 97,982
	Good bases (pairs): 19,792,364
	Good mean length (pairs): 202.00
	Good sequences (singletons file 1): 1,078 (1.08%)
	Good bases (singletons file 1): 108,878
	Good mean length (singletons file 1): 101.00
	Good sequences (singletons file 2): 364 (0.36%)
	Good bases (singletons file 2): 36,764
	Good mean length (singletons file 2): 101.00
	Bad sequences (file 1): 940 (0.94%)
	Bad bases (file 1): 94,940
	Bad mean length (file 1): 101.00
	Bad sequences (file 2): 1,078 (1.08%)
	Bad bases (file 2): 108,878
	Bad mean length (file 2): 101.00
	Sequences filtered by specified parameters:
	trim_qual_right: 233
	trim_tail_right: 14
	min_len: 1177
	ns_max_p: 1170
+ rm -f output.prinseq/SRR4425244_1.fastq_1_singletons.fastq output.prinseq/SRR4425244_1.fastq_2_singletons.fastq output.prinseq/SRR4425245_1.fastq_1_singletons.fastq output.prinseq/SRR4425245_1.fastq_2_singletons.fastq output.prinseq/SRR4425248_1.fastq_1_singletons.fastq output.prinseq/SRR4425248_1.fastq_2_singletons.fastq output.prinseq/SRR4425249_1.fastq_1_singletons.fastq output.prinseq/SRR4425249_1.fastq_2_singletons.fastq output.prinseq/SRR4425250_1.fastq_1_singletons.fastq output.prinseq/SRR4425250_1.fastq_2_singletons.fastq output.prinseq/SRR4425251_1.fastq_1_singletons.fastq output.prinseq/SRR4425251_1.fastq_2_singletons.fastq
++ find output.prinseq/
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
+ r1='output.prinseq/SRR4425244_1.fastq
output.prinseq/SRR4425250_1.fastq
output.prinseq/SRR4425249_1.fastq
output.prinseq/SRR4425245_1.fastq
output.prinseq/SRR4425248_1.fastq
output.prinseq/SRR4425251_1.fastq'
+ mkdir -p output.unsorted_bam
+ for i in '$r1'
+ xargs -I '{}' -P 1 bash -c '{}'
++ echo output.prinseq/SRR4425244_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/SRR4425244_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/SRR4425244_2.fastq
++ basename output.prinseq/SRR4425244_1.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x input_4/hisat2_index -1 output.prinseq/SRR4425244_1.fastq -2 output.prinseq/SRR4425244_2.fastq --rg-id output.prinseq/SRR4425244_1.fastq --rg 'SM:output.prinseq/SRR4425244_1.fastq|docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools view -@ 8 -b -o output.unsorted_bam/SRR4425244_1.fastq.bam
+ for i in '$r1'
++ echo output.prinseq/SRR4425250_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/SRR4425250_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/SRR4425250_2.fastq
++ basename output.prinseq/SRR4425250_1.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x input_4/hisat2_index -1 output.prinseq/SRR4425250_1.fastq -2 output.prinseq/SRR4425250_2.fastq --rg-id output.prinseq/SRR4425250_1.fastq --rg 'SM:output.prinseq/SRR4425250_1.fastq|docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools view -@ 8 -b -o output.unsorted_bam/SRR4425250_1.fastq.bam
+ for i in '$r1'
++ echo output.prinseq/SRR4425249_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/SRR4425249_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/SRR4425249_2.fastq
++ basename output.prinseq/SRR4425249_1.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x input_4/hisat2_index -1 output.prinseq/SRR4425249_1.fastq -2 output.prinseq/SRR4425249_2.fastq --rg-id output.prinseq/SRR4425249_1.fastq --rg 'SM:output.prinseq/SRR4425249_1.fastq|docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools view -@ 8 -b -o output.unsorted_bam/SRR4425249_1.fastq.bam
+ for i in '$r1'
++ echo output.prinseq/SRR4425245_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/SRR4425245_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/SRR4425245_2.fastq
++ basename output.prinseq/SRR4425245_1.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x input_4/hisat2_index -1 output.prinseq/SRR4425245_1.fastq -2 output.prinseq/SRR4425245_2.fastq --rg-id output.prinseq/SRR4425245_1.fastq --rg 'SM:output.prinseq/SRR4425245_1.fastq|docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools view -@ 8 -b -o output.unsorted_bam/SRR4425245_1.fastq.bam
+ for i in '$r1'
++ echo output.prinseq/SRR4425248_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/SRR4425248_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/SRR4425248_2.fastq
++ basename output.prinseq/SRR4425248_1.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x input_4/hisat2_index -1 output.prinseq/SRR4425248_1.fastq -2 output.prinseq/SRR4425248_2.fastq --rg-id output.prinseq/SRR4425248_1.fastq --rg 'SM:output.prinseq/SRR4425248_1.fastq|docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools view -@ 8 -b -o output.unsorted_bam/SRR4425248_1.fastq.bam
+ for i in '$r1'
++ echo output.prinseq/SRR4425251_1.fastq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/SRR4425251_1.fastq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/SRR4425251_2.fastq
++ basename output.prinseq/SRR4425251_1.fastq
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/hisat2:2.1.0--py27h6bb024c_3 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x input_4/hisat2_index -1 output.prinseq/SRR4425251_1.fastq -2 output.prinseq/SRR4425251_2.fastq --rg-id output.prinseq/SRR4425251_1.fastq --rg 'SM:output.prinseq/SRR4425251_1.fastq|docker' run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools view -@ 8 -b -o output.unsorted_bam/SRR4425251_1.fastq.bam
98443 reads; of these:
  98443 (100.00%) were paired; of these:
    4773 (4.85%) aligned concordantly 0 times
    89899 (91.32%) aligned concordantly exactly 1 time
    3771 (3.83%) aligned concordantly >1 times
    ----
    4773 pairs aligned concordantly 0 times; of these:
      1402 (29.37%) aligned discordantly 1 time
    ----
    3371 pairs aligned 0 times concordantly or discordantly; of these:
      6742 mates make up the pairs; of these:
        4078 (60.49%) aligned 0 times
        2462 (36.52%) aligned exactly 1 time
        202 (3.00%) aligned >1 times
97.93% overall alignment rate
98286 reads; of these:
  98286 (100.00%) were paired; of these:
    7215 (7.34%) aligned concordantly 0 times
    80455 (81.86%) aligned concordantly exactly 1 time
    10616 (10.80%) aligned concordantly >1 times
    ----
    7215 pairs aligned concordantly 0 times; of these:
      1057 (14.65%) aligned discordantly 1 time
    ----
    6158 pairs aligned 0 times concordantly or discordantly; of these:
      12316 mates make up the pairs; of these:
        10537 (85.56%) aligned 0 times
        1407 (11.42%) aligned exactly 1 time
        372 (3.02%) aligned >1 times
94.64% overall alignment rate
97935 reads; of these:
  97935 (100.00%) were paired; of these:
    4680 (4.78%) aligned concordantly 0 times
    90116 (92.02%) aligned concordantly exactly 1 time
    3139 (3.21%) aligned concordantly >1 times
    ----
    4680 pairs aligned concordantly 0 times; of these:
      1343 (28.70%) aligned discordantly 1 time
    ----
    3337 pairs aligned 0 times concordantly or discordantly; of these:
      6674 mates make up the pairs; of these:
        4197 (62.89%) aligned 0 times
        2273 (34.06%) aligned exactly 1 time
        204 (3.06%) aligned >1 times
97.86% overall alignment rate
97729 reads; of these:
  97729 (100.00%) were paired; of these:
    4281 (4.38%) aligned concordantly 0 times
    88214 (90.26%) aligned concordantly exactly 1 time
    5234 (5.36%) aligned concordantly >1 times
    ----
    4281 pairs aligned concordantly 0 times; of these:
      1019 (23.80%) aligned discordantly 1 time
    ----
    3262 pairs aligned 0 times concordantly or discordantly; of these:
      6524 mates make up the pairs; of these:
        4131 (63.32%) aligned 0 times
        2176 (33.35%) aligned exactly 1 time
        217 (3.33%) aligned >1 times
97.89% overall alignment rate
97562 reads; of these:
  97562 (100.00%) were paired; of these:
    4569 (4.68%) aligned concordantly 0 times
    89642 (91.88%) aligned concordantly exactly 1 time
    3351 (3.43%) aligned concordantly >1 times
    ----
    4569 pairs aligned concordantly 0 times; of these:
      1236 (27.05%) aligned discordantly 1 time
    ----
    3333 pairs aligned 0 times concordantly or discordantly; of these:
      6666 mates make up the pairs; of these:
        4068 (61.03%) aligned 0 times
        2355 (35.33%) aligned exactly 1 time
        243 (3.65%) aligned >1 times
97.92% overall alignment rate
97982 reads; of these:
  97982 (100.00%) were paired; of these:
    7981 (8.15%) aligned concordantly 0 times
    77417 (79.01%) aligned concordantly exactly 1 time
    12584 (12.84%) aligned concordantly >1 times
    ----
    7981 pairs aligned concordantly 0 times; of these:
      1371 (17.18%) aligned discordantly 1 time
    ----
    6610 pairs aligned 0 times concordantly or discordantly; of these:
      13220 mates make up the pairs; of these:
        11348 (85.84%) aligned 0 times
        1417 (10.72%) aligned exactly 1 time
        455 (3.44%) aligned >1 times
94.21% overall alignment rate
+ rm -rf output.prinseq
+ mkdir -p output.sorted_bam
++ echo 67108864
++ awk -v N_CPU=8 '{print int($1/1024/N_CPU*0.8)}'
+ MEMM=6553
+ xargs -I '{}' -P 1 bash -c '{}'
+ for i in 'output.unsorted_bam/*.bam'
++ basename output.unsorted_bam/SRR4425244_1.fastq.bam
++ basename output.unsorted_bam/SRR4425244_1.fastq.bam
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools sort -m 6553M -@ 8 -o output.sorted_bam/SRR4425244_1.fastq.bam 'output.unsorted_bam/SRR4425244_1.fastq.bam;' docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools index output.sorted_bam/SRR4425244_1.fastq.bam
+ for i in 'output.unsorted_bam/*.bam'
++ basename output.unsorted_bam/SRR4425245_1.fastq.bam
++ basename output.unsorted_bam/SRR4425245_1.fastq.bam
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools sort -m 6553M -@ 8 -o output.sorted_bam/SRR4425245_1.fastq.bam 'output.unsorted_bam/SRR4425245_1.fastq.bam;' docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools index output.sorted_bam/SRR4425245_1.fastq.bam
+ for i in 'output.unsorted_bam/*.bam'
++ basename output.unsorted_bam/SRR4425248_1.fastq.bam
++ basename output.unsorted_bam/SRR4425248_1.fastq.bam
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools sort -m 6553M -@ 8 -o output.sorted_bam/SRR4425248_1.fastq.bam 'output.unsorted_bam/SRR4425248_1.fastq.bam;' docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools index output.sorted_bam/SRR4425248_1.fastq.bam
+ for i in 'output.unsorted_bam/*.bam'
++ basename output.unsorted_bam/SRR4425249_1.fastq.bam
++ basename output.unsorted_bam/SRR4425249_1.fastq.bam
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools sort -m 6553M -@ 8 -o output.sorted_bam/SRR4425249_1.fastq.bam 'output.unsorted_bam/SRR4425249_1.fastq.bam;' docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools index output.sorted_bam/SRR4425249_1.fastq.bam
+ for i in 'output.unsorted_bam/*.bam'
++ basename output.unsorted_bam/SRR4425250_1.fastq.bam
++ basename output.unsorted_bam/SRR4425250_1.fastq.bam
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools sort -m 6553M -@ 8 -o output.sorted_bam/SRR4425250_1.fastq.bam 'output.unsorted_bam/SRR4425250_1.fastq.bam;' docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools index output.sorted_bam/SRR4425250_1.fastq.bam
+ for i in 'output.unsorted_bam/*.bam'
++ basename output.unsorted_bam/SRR4425251_1.fastq.bam
++ basename output.unsorted_bam/SRR4425251_1.fastq.bam
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools sort -m 6553M -@ 8 -o output.sorted_bam/SRR4425251_1.fastq.bam 'output.unsorted_bam/SRR4425251_1.fastq.bam;' docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 samtools index output.sorted_bam/SRR4425251_1.fastq.bam
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
+ 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/69:/data/user2/work/69 -w /data/user2/work/69 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit