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
using docker
+ set -o pipefail
++ echo input_1/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_1/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_1/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ sed 's/[.]\(gff\|gff3\)$/.gtf/'
+ temp_1=input_1/Bomo_gene_models.withnote.plus.NC_002355.gtf
++ echo input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ sed 's/[.]\(gff\|gff3\)$/.withname.gtf/'
+ temp_2=input_1/Bomo_gene_models.withnote.plus.NC_002355.withname.gtf
+ docker run -v /data/user2/work/71:/data/user2/work/71 -w /data/user2/work/71 -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_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.rename /dev/stdout
+ docker run -v /data/user2/work/71:/data/user2/work/71 -w /data/user2/work/71 -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_1/Bomo_gene_models.withnote.plus.NC_002355.gtf
+ sed 's/ \+/ /g' input_1/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_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.rename /dev/stdin
+ 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/71:/data/user2/work/71 -w /data/user2/work/71 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit