script: annotation~blast "$scriptdir"/preprocessing~extract-only-specific-entries-in-FASTA
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/blast:2.9.0--pl526h979a64d_3
using docker
++ docker pull quay.io/biocontainers/blast:2.9.0--pl526h979a64d_3
2.9.0--pl526h979a64d_3: Pulling from biocontainers/blast
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
ca8b68c6162b: Pulling fs layer
ca8b68c6162b: Verifying Checksum
ca8b68c6162b: Download complete
ca8b68c6162b: Pull complete
Digest: sha256:7adc4761b5645fab73aa3b094f20d9622d84828978624734fb4d3a13cf4ba7ae
Status: Downloaded newer image for quay.io/biocontainers/blast:2.9.0--pl526h979a64d_3
++ set +ex
+ set -o pipefail
+ query=input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta
+ db=input_2/dmel-all-translation-r6.29.fasta
+ table=input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt
+ '[' blastx = blastn -o blastx = tblastn -o blastx = tblastx ']'
+ '[' blastx = blastp -o blastx = blastx ']'
+ dbtype=prot
+ docker run -v /data/user2/work/74:/data/user2/work/74 -w /data/user2/work/74 -u root -i --rm quay.io/biocontainers/blast:2.9.0--pl526h979a64d_3 makeblastdb -in input_2/dmel-all-translation-r6.29.fasta -dbtype prot


Building a new DB, current time: 09/06/2019 07:45:02
New DB name:   /data/user2/work/74/input_2/dmel-all-translation-r6.29.fasta
New DB title:  input_2/dmel-all-translation-r6.29.fasta
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 30597 sequences in 1.44444 seconds.
++ basename input_2/dmel-all-translation-r6.29.fasta
++ basename input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta
+ output=dmel-all-translation-r6.29.fasta.Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta.blastx
+ '[' input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt = '' ']'
+ bash /data/user2/work/74/preprocessing~extract-only-specific-entries-in-FASTA input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt
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/blast:2.9.0--pl526h979a64d_3
using docker
+ set -o pipefail
+ fasta=input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta
+ table=input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt
++ basename input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes
++ basename input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down
+ output=Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.fasta
+ sed 's/\r//' input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt
+ docker run -v /data/user2/work/74:/data/user2/work/74 -w /data/user2/work/74 -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 input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta
+ docker run -v /data/user2/work/74:/data/user2/work/74 -w /data/user2/work/74 -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' '
  FILENAME==ARGV[1]{split($1,arr," "); flag[arr[1]]=1}
  FILENAME==ARGV[2]{split($1,arr," "); if(flag[arr[1]]==1){print ">"$1; print $2}}
 ' input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt.temp /dev/stdin
+ post_processing
+ '[' 2 = 1 ']'
+ exit
++ basename input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes
++ basename input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down
+ newquery=Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.fasta
+ docker run -v /data/user2/work/74:/data/user2/work/74 -w /data/user2/work/74 -u root -i --rm quay.io/biocontainers/blast:2.9.0--pl526h979a64d_3 blastx -db input_2/dmel-all-translation-r6.29.fasta -query Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.fasta -num_threads 8 -outfmt 6
+ awk '-F\t' '
  FILENAME==ARGV[1]{if(data[$1]==""){data[$1]=$2; evalue[$1]=$11}}
  FILENAME==ARGV[2]{if($0~"^>"){split($0,arr,"[ \t]"); desc[substr(arr[1],2)]=substr($0,2)}}
  FILENAME==ARGV[3]{if(FNR==1){print $0"\tTop Hit ("ARGV[1]")\te-value"}else{print $0"\t"desc[data[$1]]"\t"evalue[$1]}}
 ' dmel-all-translation-r6.29.fasta.Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta.blastx input_2/dmel-all-translation-r6.29.fasta input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt.temp
++ basename input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt
++ basename input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt
++ basename input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt
+ docker run -v /data/user2/work/74:/data/user2/work/74 -w /data/user2/work/74 -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 java -Xmx1G -jar /usr/local/bin/excel2.jar result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt.blastx.txt result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt.blastx.xlsx
Start converting
+ 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/74:/data/user2/work/74 -w /data/user2/work/74 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit