c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 centos:centos6 quay.io/biocontainers/cufflinks:2.2.1--py36_1
using docker
++ docker pull quay.io/biocontainers/cufflinks:2.2.1--py36_1
2.2.1--py36_1: Pulling from biocontainers/cufflinks
a3ed95caeb02: Already exists
77c6c00e8b61: Already exists
3aaade50789a: Already exists
00cf8b9f3d2a: Already exists
7ff999a2256f: Already exists
d2ba336f2e44: Already exists
dfda3e01f2b6: Already exists
a3ed95caeb02: Already exists
10c3bb32200b: Already exists
72103a677086: Pulling fs layer
72103a677086: Verifying Checksum
72103a677086: Download complete
72103a677086: Pull complete
Digest: sha256:4dd5c7d799091aef33bc8dfeb46bcd8213e154c83fc5081695f7c56f58d34a79
Status: Downloaded newer image for quay.io/biocontainers/cufflinks:2.2.1--py36_1
++ set +ex
+ set -o pipefail
++ echo input_1/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_2/Bomo_gene_models.withnote.plus.NC_002355.gff3
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ basename input_2/Bomo_gene_models.withnote.plus.NC_002355.gff3
+ output=Bomo_gene_models.withnote.plus.NC_002355.gff3.with-genename.transcripts.fasta
++ basename input_2/Bomo_gene_models.withnote.plus.NC_002355.gff3
+ outputid=Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.transcripts.fasta
++ basename input_2/Bomo_gene_models.withnote.plus.NC_002355.gff3
+ output2=Bomo_gene_models.withnote.plus.NC_002355.gff3.with-genename.genes.fasta
++ basename input_2/Bomo_gene_models.withnote.plus.NC_002355.gff3
+ outputid2=Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta
+ docker run -v /data/user2/work/73:/data/user2/work/73 -w /data/user2/work/73 -u root -i --rm quay.io/biocontainers/cufflinks:2.2.1--py36_1 gffread -g input_1/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa -w Bomo_gene_models.withnote.plus.NC_002355.gff3.with-genename.transcripts.fasta input_2/Bomo_gene_models.withnote.plus.NC_002355.gff3
No fasta index found for input_1/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa. Rebuilding, please wait..
Fasta index rebuilt.
Error (GFaSeqGet): end coordinate (15883) cannot be larger than sequence length 15643
+ awk '-F\t' '$3=="gene"{
  split($9,arr,";"); id=""; name=""; for(i in arr){if(arr[i]~"^ID="){id=substr(arr[i],4)}else if(arr[i]~"^Name="){name=substr(arr[i],6)}}; print id"\t"name
 }' input_2/Bomo_gene_models.withnote.plus.NC_002355.gff3
+ awk '-F\t' '
  FILENAME==ARGV[1]{id[$2]=$1}
  FILENAME==ARGV[2]{
   if($0~"^>"){split($0,arr," "); split(arr[2],arr2,"="); if(id[arr2[2]]!=""){arr[2]="gene="id[arr2[2]]}; print arr[1]" "arr[2]" "arr[3]}else{print $0}
  }' /dev/stdin Bomo_gene_models.withnote.plus.NC_002355.gff3.with-genename.transcripts.fasta
+ docker run -v /data/user2/work/73:/data/user2/work/73 -w /data/user2/work/73 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 /usr/local/trinityrnaseq-Trinity-v2.8.5/util/support_scripts/fasta_to_tab.pl Bomo_gene_models.withnote.plus.NC_002355.gff3.with-genename.transcripts.fasta
+ docker run -v /data/user2/work/73:/data/user2/work/73 -w /data/user2/work/73 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 awk '-F\t' '
 {
  split($1,arr," "); gene=""; for(i in arr){if(arr[i]~"^gene="){gene=substr(arr[i],6)}};
  name=arr[1]; if(gene!=""){name=gene}; len[name][arr[1]]=length($2); seq[arr[1]]=$2
 }
 END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in len){for(j in len[i]){print ">"i" transcript="j; print seq[j]; break}}}
'
+ docker run -v /data/user2/work/73:/data/user2/work/73 -w /data/user2/work/73 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 /usr/local/trinityrnaseq-Trinity-v2.8.5/util/support_scripts/fasta_to_tab.pl Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.transcripts.fasta
+ docker run -v /data/user2/work/73:/data/user2/work/73 -w /data/user2/work/73 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 awk '-F\t' '
 {
  split($1,arr," "); gene=""; for(i in arr){if(arr[i]~"^gene="){gene=substr(arr[i],6)}};
  name=arr[1]; if(gene!=""){name=gene}; len[name][arr[1]]=length($2); seq[arr[1]]=$2
 }
 END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in len){for(j in len[i]){print ">"i" transcript="j; print seq[j]; break}}}
'
+ 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/73:/data/user2/work/73 -w /data/user2/work/73 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit