c2997108/centos7:2 centos:centos6 quay.io/biocontainers/subread:1.6.3--h84994c4_1 using docker + set -o pipefail ++ echo input_2/Bomo_gene_models.withnote.plus.NC_002355.gtf ++ grep '[.]gz$' ++ wc -l ++ true + '[' 0 = 1 ']' + docker run -v /data/user2/work/70:/data/user2/work/70 -w /data/user2/work/70 -u root -i --rm quay.io/biocontainers/subread:1.6.3--h84994c4_1 featureCounts -p -t exon -g gene_id -T 8 -a input_2/Bomo_gene_models.withnote.plus.NC_002355.gtf -o count.id.txt input_1/SRR4425244_1.fastq.bam input_1/SRR4425245_1.fastq.bam input_1/SRR4425248_1.fastq.bam input_1/SRR4425249_1.fastq.bam input_1/SRR4425250_1.fastq.bam input_1/SRR4425251_1.fastq.bam ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== featureCounts setting ===========================\\ || || || Input files : 6 BAM files || || P SRR4425244_1.fastq.bam || || P SRR4425245_1.fastq.bam || || P SRR4425248_1.fastq.bam || || P SRR4425249_1.fastq.bam || || P SRR4425250_1.fastq.bam || || P SRR4425251_1.fastq.bam || || || || Output file : count.id.txt || || Summary : count.id.txt.summary || || Annotation : Bomo_gene_models.withnote.plus.NC_002355.gtf ... || || Dir for temp files : ./ || || || || Threads : 8 || || Level : meta-feature level || || Paired-end : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || || Chimeric reads : counted || || Both ends mapped : not required || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Bomo_gene_models.withnote.plus.NC_002355.gtf ... || || Features : 102293 || || Meta-features : 16917 || || Chromosomes/contigs : 230 || || || || Process BAM file SRR4425244_1.fastq.bam... || || Paired-end reads are included. || || Assign alignments (paired-end) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total alignments : 113885 || || Successfully assigned alignments : 66002 (58.0%) || || Running time : 0.01 minutes || || || || Process BAM file SRR4425245_1.fastq.bam... || || Paired-end reads are included. || || Assign alignments (paired-end) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total alignments : 121255 || || Successfully assigned alignments : 66737 (55.0%) || || Running time : 0.01 minutes || || || || Process BAM file SRR4425248_1.fastq.bam... || || Paired-end reads are included. || || Assign alignments (paired-end) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total alignments : 110176 || || Successfully assigned alignments : 76723 (69.6%) || || Running time : 0.01 minutes || || || || Process BAM file SRR4425249_1.fastq.bam... || || Paired-end reads are included. || || Assign alignments (paired-end) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total alignments : 110179 || || Successfully assigned alignments : 80736 (73.3%) || || Running time : 0.01 minutes || || || || Process BAM file SRR4425250_1.fastq.bam... || || Paired-end reads are included. || || Assign alignments (paired-end) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total alignments : 135868 || || Successfully assigned alignments : 37622 (27.7%) || || Running time : 0.01 minutes || || || || Process BAM file SRR4425251_1.fastq.bam... || || Paired-end reads are included. || || Assign alignments (paired-end) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total alignments : 144290 || || Successfully assigned alignments : 36041 (25.0%) || || Running time : 0.01 minutes || || || || || || Summary of counting results can be found in file "count.id.txt.summary" || || || \\===================== http://subread.sourceforge.net/ ======================// + awk '-F\t' '$3=="gene" || $3=="transcript"{print $0}' input_2/Bomo_gene_models.withnote.plus.NC_002355.gtf + grep 'gene_id ' + grep '; *gene_name ' + sed 's/.*gene_id "//; s/".*; *gene_name "/\t/; s/".*//' + awk '-F\t' ' BEGIN{OFS="\t"; name["Geneid"]="name"} FILENAME==ARGV[1]{name[$1]=$2} FILENAME==ARGV[2] && FNR>1{if(FNR==2){for(i=7;i<=NF;i++){split($i,arr,"/"); $i=arr[length(arr)]}}; $1=$1"\t"name[$1]; print $0} ' /dev/stdin count.id.txt + head -n 2 count.id.txt.summary + docker run -v /data/user2/work/70:/data/user2/work/70 -w /data/user2/work/70 -u root -i --rm c2997108/centos7:2 trans-row-column.sh - + awk -F/ '{print $NF}' + awk '-F\t' ' FILENAME==ARGV[1]{cnt[$1]=$2; if(cnt[$1]==0){cnt[$1]=1}} FILENAME==ARGV[2]{if(FNR==1){for(i=8;i<=NF;i++){name[i]=$i}; OFS="\t"}else{for(i=8;i<=NF;i++){$i=$i/cnt[name[i]]*1000*1000/$7*1000}}; print $0} ' /dev/stdin count.id-genename.txt + awk '-F\t' '{OFS="\t"; if($2!=""){$7=$2"_"$1}else{$7=$1}; print $0}' count.id-genename.txt + cut -f 7- + cut -f 1,8- count.id-genename.txt + 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/70:/data/user2/work/70 -w /data/user2/work/70 -u root -i --rm centos:centos6 chmod -R a=rXw . + echo 0 + exit