/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'annotation~Helixer' -c 8 -m 32 -l invertebrate_v0.3_m_0200.h5 -s 21384 input_1/parasite.fa
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/annotation~Helixer
Containers: biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/helixer:v0.3.4_cuda_12.2.2-cudnn8 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/seqkit:0.12.1--0
Checking singularity
WARNING: passwd file doesn't exist in container, not updating
WARNING: group file doesn't exist in container, not updating
using singularity
++ set -o pipefail
+ set -eux
+ set -o pipefail
++ echo input_1/parasite.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_1/parasite.fa
+ sed 's/\r//'
+ input_1=input_1/parasite.fa.ref.fa
+ singularity exec --no-home -B /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer:/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer --pwd /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer -B /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi /home/yoshitake.kazutoshi/img/quay.io/biocontainers/gffread:0.12.7--h9a82719_0 gffread -g input_1/parasite.fa.ref.fa -w helixer.exons.fasta -x helixer.cds.fasta helixer.gff3
+ singularity exec --no-home -B /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer:/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer --pwd /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer -B /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi /home/yoshitake.kazutoshi/img/biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 transeq -sequence helixer.cds.fasta -outseq tmp.helixer.cds.aa.fasta -frame 1
Translate nucleic acid sequences
+ singularity exec --no-home -B /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer:/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer --pwd /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer -B /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi /home/yoshitake.kazutoshi/img/quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab tmp.helixer.cds.aa.fasta
+ singularity exec --no-home -B /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer:/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer --pwd /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer -B /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi /home/yoshitake.kazutoshi/img/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' '{sub(/_1$/,"",$1); sub(/*$/,"",$(NF-1)); print ">"$1; print $(NF-1)}'
WARNING: Skipping mount /suikou/tool9/apptainer_v2023-07-21/x86_64/var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
+ rm -f tmp.helixer.cds.aa.fasta
+ singularity exec --no-home -B /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer:/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer --pwd /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer -B /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi /home/yoshitake.kazutoshi/img/quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab helixer.cds.aa.fasta
+ awk '-F\t' 'FILENAME==ARGV[1]{name[$1]=$2; desc[$1]=$16; evalue[$1]=$13} FILENAME==ARGV[2]{print ">"$1" "name[$1]":"desc[$1]" evalue:"evalue[$1]; print $2}' helixer.cds.aa.fasta.uniprot.blastp /dev/stdin
WARNING: Skipping mount /suikou/tool9/apptainer_v2023-07-21/x86_64/var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
+ singularity exec --no-home -B /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer:/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer --pwd /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer -B /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi /home/yoshitake.kazutoshi/img/quay.io/biocontainers/seqkit:0.12.1--0 seqkit fx2tab helixer.cds.fasta
+ awk '-F\t' 'FILENAME==ARGV[1]{name[$1]=$2; desc[$1]=$16; evalue[$1]=$13} FILENAME==ARGV[2]{split($1,arr," "); print ">"$1" "name[arr[1]]":"desc[arr[1]]" evalue:"evalue[arr[1]]; print $2}' helixer.cds.aa.fasta.uniprot.blastp /dev/stdin
WARNING: Skipping mount /suikou/tool9/apptainer_v2023-07-21/x86_64/var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
+ singularity exec --no-home -B /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer:/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer --pwd /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer -B /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi /home/yoshitake.kazutoshi/img/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]&&!($1 in name){name[$1]=$2; desc[$1]=$16; evalue[$1]=$13; newname[$1]=$1"_"$2"_"$16"_evalue-"$13; gsub(/[ /()=]/,"_",newname[$1])} FILENAME==ARGV[2]{OFS="\t"; if($0~"^#"){print $0}else{split($9,arr,";"); for(i in arr){split(arr[i],arr2,"="); str2=arr2[2]; for(j=3;j<=length(arr2);j++){str2=str2"="arr2[j]}; if(str2 in newname){arr[i]=arr2[1]"="newname[str2]}}; $9=arr[1]; for(i=2;i<=length(arr);i++){$9=$9";"arr[i]}; print $0}}' helixer.cds.aa.fasta.uniprot.blastp helixer.gff3
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/annotation~Helixer/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit