biocontainers/samtools:v1.7.0_cv4 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 quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 quay.io/biocontainers/exonerate:2.2.0--1 quay.io/biocontainers/gatk4:4.1.0.0--0 quay.io/biocontainers/picard:2.18.27--0 quay.io/biocontainers/trinity:2.8.4--py36pl526h447964c_0 using singularity + set -o pipefail ++ echo input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa ++ grep '[.]gz$' ++ wc -l ++ true + '[' 0 = 1 ']' ++ echo input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa ++ sed 's/[.]\(fa\|fasta\|fsa\|fna\)$//' + refbase=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re + '[' -e input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.dict ']' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 picard CreateSequenceDictionary R=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa O=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.dict /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory INFO 2019-09-17 17:27:09 CreateSequenceDictionary ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CreateSequenceDictionary -R input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa -O input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.dict ********** 17:27:10.257 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Tue Sep 17 17:27:10 GMT 2019] CreateSequenceDictionary OUTPUT=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.dict REFERENCE=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Sep 17 17:27:11 GMT 2019] Executing as user2@m64 on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT [Tue Sep 17 17:27:17 GMT 2019] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=536870912 + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools faidx input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/trinity:2.8.4--py36pl526h447964c_0 /usr/local/opt/trinity-2.8.4/util/support_scripts/fasta_to_tab.pl input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "ja_JP.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). + awk '{print length($NF)"\t"$1"\t"$NF}' input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.tab + sort -nr + awk '{if($1>1000*1000){print ">"$2; print $3; print $2"\t"$2"\t1\t"$1 > "pseudochr.txt"}else{if(n==0 || n>10*1000*1000){m++; n=1; print ">pseudochr"m}else{n+=200*50; for(i=0;i<200;i++){print "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"}}; print $3; print $2"\tpseudochr"m"\t"n"\t"n+$1-1 > "pseudochr.txt"; n+=$1}}' + awk '{print $2"\t"$3-1"\t"$4"\t"$1"\t0\t+"}' + cat pseudochr.txt + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/exonerate:2.2.0--1 fastareformat pseudochr.fa + rm -f pseudochr.fa + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools faidx pseudochr.re.fa + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa index pseudochr.re.fa [bwa_index] Pack FASTA... 6.42 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=933844180, availableWord=77708540 [BWTIncConstructFromPacked] 10 iterations done. 99999988 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999988 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 298922708 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 388563188 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 468231908 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 539037668 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 601965988 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 657892836 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 707596756 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 751769716 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 791026708 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 825914420 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 856918628 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 884471252 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 908956068 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 930714196 characters processed. [bwt_gen] Finished constructing BWT in 162 iterations. [bwa_index] 416.73 seconds elapse. [bwa_index] Update BWT... 5.27 sec [bwa_index] Pack forward-only FASTA... 4.75 sec [bwa_index] Construct SA from BWT and Occ... 193.86 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index pseudochr.re.fa [main] Real time: 720.837 sec; CPU: 627.266 sec + '[' -e pseudochr.re.dict ']' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 picard CreateSequenceDictionary R=pseudochr.re.fa O=pseudochr.re.dict /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory INFO 2019-09-17 17:42:21 CreateSequenceDictionary ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CreateSequenceDictionary -R pseudochr.re.fa -O pseudochr.re.dict ********** 17:42:22.544 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Tue Sep 17 17:42:22 GMT 2019] CreateSequenceDictionary OUTPUT=pseudochr.re.dict REFERENCE=pseudochr.re.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Sep 17 17:42:22 GMT 2019] Executing as user2@m64 on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT [Tue Sep 17 17:42:27 GMT 2019] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.09 minutes. Runtime.totalMemory()=536870912 + ref=pseudochr.re.fa ++ echo 33554432 ++ awk -v N_CPU=4 '{print int($1/1024/1024/N_CPU*0.8)}' + MEMG=6 + mkdir -p output.bwa + grep submitted ++ find input_1/ ++ egrep '(_R1.*|_1)[.]f(ast|)q(|[.]gz)$' ++ echo /suikou/files/m64g/user2/work/100 ++ sed 's/^[^a-zA-Z]/_/' ++ sed 's/[^a-zA-Z0-9]/_/g' + xargs -I '{}' bash -c 'qsub -N _suikou_files_m64g_user2_work_100 -j y /suikou/files/m64g/user2/work/100/qsub.sh "{}"' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030442_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030442_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030442_2.fastq.gz ++ basename input_1/DRR030442_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030442 ++ basename input_1/DRR030442_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030442 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030442\\tSM:DRR030442\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030442_1.fastq.gz\'\'' \'\''input_1/DRR030442_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030442\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030442\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030442\'\''.bam -O \'\''output.bwa/DRR030442\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030431_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030431_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030431_2.fastq.gz ++ basename input_1/DRR030431_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030431 ++ basename input_1/DRR030431_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030431 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030431\\tSM:DRR030431\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030431_1.fastq.gz\'\'' \'\''input_1/DRR030431_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030431\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030431\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030431\'\''.bam -O \'\''output.bwa/DRR030431\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030434_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030434_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030434_2.fastq.gz ++ basename input_1/DRR030434_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030434 ++ basename input_1/DRR030434_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030434 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030434\\tSM:DRR030434\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030434_1.fastq.gz\'\'' \'\''input_1/DRR030434_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030434\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030434\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030434\'\''.bam -O \'\''output.bwa/DRR030434\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030437_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030437_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030437_2.fastq.gz ++ basename input_1/DRR030437_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030437 ++ basename input_1/DRR030437_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030437 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030437\\tSM:DRR030437\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030437_1.fastq.gz\'\'' \'\''input_1/DRR030437_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030437\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030437\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030437\'\''.bam -O \'\''output.bwa/DRR030437\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030436_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030436_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030436_2.fastq.gz ++ basename input_1/DRR030436_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030436 ++ basename input_1/DRR030436_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030436 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030436\\tSM:DRR030436\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030436_1.fastq.gz\'\'' \'\''input_1/DRR030436_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030436\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030436\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030436\'\''.bam -O \'\''output.bwa/DRR030436\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030438_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030438_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030438_2.fastq.gz ++ basename input_1/DRR030438_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030438 ++ basename input_1/DRR030438_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030438 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030438\\tSM:DRR030438\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030438_1.fastq.gz\'\'' \'\''input_1/DRR030438_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030438\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030438\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030438\'\''.bam -O \'\''output.bwa/DRR030438\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030441_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030441_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030441_2.fastq.gz ++ basename input_1/DRR030441_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030441 ++ basename input_1/DRR030441_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030441 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030441\\tSM:DRR030441\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030441_1.fastq.gz\'\'' \'\''input_1/DRR030441_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030441\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030441\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030441\'\''.bam -O \'\''output.bwa/DRR030441\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030439_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030439_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030439_2.fastq.gz ++ basename input_1/DRR030439_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030439 ++ basename input_1/DRR030439_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030439 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030439\\tSM:DRR030439\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030439_1.fastq.gz\'\'' \'\''input_1/DRR030439_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030439\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030439\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030439\'\''.bam -O \'\''output.bwa/DRR030439\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030433_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030433_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030433_2.fastq.gz ++ basename input_1/DRR030433_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030433 ++ basename input_1/DRR030433_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030433 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030433\\tSM:DRR030433\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030433_1.fastq.gz\'\'' \'\''input_1/DRR030433_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030433\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030433\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030433\'\''.bam -O \'\''output.bwa/DRR030433\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030435_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030435_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030435_2.fastq.gz ++ basename input_1/DRR030435_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030435 ++ basename input_1/DRR030435_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030435 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030435\\tSM:DRR030435\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030435_1.fastq.gz\'\'' \'\''input_1/DRR030435_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030435\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030435\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030435\'\''.bam -O \'\''output.bwa/DRR030435\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030432_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030432_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030432_2.fastq.gz ++ basename input_1/DRR030432_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030432 ++ basename input_1/DRR030432_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030432 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030432\\tSM:DRR030432\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030432_1.fastq.gz\'\'' \'\''input_1/DRR030432_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030432\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030432\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030432\'\''.bam -O \'\''output.bwa/DRR030432\'\''.g.vcf.gz -ERC GVCF' + for i in '`find $input_1/ |egrep '\''(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'\''`' ++ echo input_1/DRR030440_1.fastq.gz ++ egrep '_1[.]f(ast|)q(|[.]gz)$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030440_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + i2=input_1/DRR030440_2.fastq.gz ++ basename input_1/DRR030440_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + outbase=output.bwa/DRR030440 ++ basename input_1/DRR030440_1.fastq.gz ++ sed 's/_1[.]f.*//' ++ sed 's/_R1.*//' + samplename=DRR030440 + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa mem -t 4 -R \'\''@RG\\tID:DRR030440\\tSM:DRR030440\\tLB:library\'\'' \'\''pseudochr.re.fa\'\'' \'\''input_1/DRR030440_1.fastq.gz\'\'' \'\''input_1/DRR030440_2.fastq.gz\'\'' | singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools sort -@ 4 -o \'\''output.bwa/DRR030440\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools index \'\''output.bwa/DRR030440\'\''.bam; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' HaplotypeCaller -R \'\''pseudochr.re.fa\'\'' -I \'\''output.bwa/DRR030440\'\''.bam -O \'\''output.bwa/DRR030440\'\''.g.vcf.gz -ERC GVCF' + grep submitted ++ echo /suikou/files/m64g/user2/work/100 ++ sed 's/[^a-zA-Z0-9]/_/g' ++ sed 's/^[^a-zA-Z]/_/' + qsub -hold_jid _suikou_files_m64g_user2_work_100 /suikou/files/m64g/user2/work/100/qsub.sh touch /suikou/files/m64g/user2/work/100/fin + set +x + ls output.bwa/DRR030431.g.vcf.gz output.bwa/DRR030432.g.vcf.gz output.bwa/DRR030433.g.vcf.gz output.bwa/DRR030434.g.vcf.gz output.bwa/DRR030435.g.vcf.gz output.bwa/DRR030436.g.vcf.gz output.bwa/DRR030437.g.vcf.gz output.bwa/DRR030438.g.vcf.gz output.bwa/DRR030439.g.vcf.gz output.bwa/DRR030440.g.vcf.gz output.bwa/DRR030441.g.vcf.gz output.bwa/DRR030442.g.vcf.gz + cat gvcf.list.txt + sed 's%output.bwa/%%; s/.g.vcf.gz//' + paste gvcf.list.txt2 gvcf.list.txt + mkdir -p output.gatk + grep submitted ++ echo /suikou/files/m64g/user2/work/100 ++ cat pseudochr.re.fa.fai ++ cut -f 1 ++ sed 's/^[^a-zA-Z]/_/' ++ sed 's/[^a-zA-Z0-9]/_/g' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr23 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr23 --batch-size 5 -L Bomo_Chr23 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr23.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr23 -L Bomo_Chr23' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr1 ']' + xargs -I '{}' bash -c 'qsub -N _suikou_files_m64g_user2_work_100 -j y /suikou/files/m64g/user2/work/100/qsub.sh "{}"' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr1 --batch-size 5 -L Bomo_Chr1 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr1.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr1 -L Bomo_Chr1' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr11 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr11 --batch-size 5 -L Bomo_Chr11 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr11.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr11 -L Bomo_Chr11' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr5 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr5 --batch-size 5 -L Bomo_Chr5 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr5.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr5 -L Bomo_Chr5' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr4 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr4 --batch-size 5 -L Bomo_Chr4 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr4.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr4 -L Bomo_Chr4' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr22 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr22 --batch-size 5 -L Bomo_Chr22 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr22.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr22 -L Bomo_Chr22' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr15 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr15 --batch-size 5 -L Bomo_Chr15 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr15.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr15 -L Bomo_Chr15' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr13 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr13 --batch-size 5 -L Bomo_Chr13 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr13.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr13 -L Bomo_Chr13' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr10 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr10 --batch-size 5 -L Bomo_Chr10 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr10.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr10 -L Bomo_Chr10' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr12 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr12 --batch-size 5 -L Bomo_Chr12 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr12.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr12 -L Bomo_Chr12' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr24 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr24 --batch-size 5 -L Bomo_Chr24 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr24.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr24 -L Bomo_Chr24' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr17 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr17 --batch-size 5 -L Bomo_Chr17 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr17.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr17 -L Bomo_Chr17' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr9 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr9 --batch-size 5 -L Bomo_Chr9 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr9.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr9 -L Bomo_Chr9' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr6 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr6 --batch-size 5 -L Bomo_Chr6 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr6.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr6 -L Bomo_Chr6' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr8 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr8 --batch-size 5 -L Bomo_Chr8 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr8.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr8 -L Bomo_Chr8' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr18 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr18 --batch-size 5 -L Bomo_Chr18 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr18.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr18 -L Bomo_Chr18' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr21 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr21 --batch-size 5 -L Bomo_Chr21 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr21.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr21 -L Bomo_Chr21' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr3 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr3 --batch-size 5 -L Bomo_Chr3 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr3.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr3 -L Bomo_Chr3' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr19 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr19 --batch-size 5 -L Bomo_Chr19 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr19.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr19 -L Bomo_Chr19' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr25 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr25 --batch-size 5 -L Bomo_Chr25 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr25.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr25 -L Bomo_Chr25' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr16 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr16 --batch-size 5 -L Bomo_Chr16 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr16.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr16 -L Bomo_Chr16' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr7 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr7 --batch-size 5 -L Bomo_Chr7 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr7.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr7 -L Bomo_Chr7' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr14 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr14 --batch-size 5 -L Bomo_Chr14 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr14.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr14 -L Bomo_Chr14' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr20 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr20 --batch-size 5 -L Bomo_Chr20 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr20.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr20 -L Bomo_Chr20' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr26 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr26 --batch-size 5 -L Bomo_Chr26 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr26.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr26 -L Bomo_Chr26' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr27 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr27 --batch-size 5 -L Bomo_Chr27 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr27.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr27 -L Bomo_Chr27' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr28 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr28 --batch-size 5 -L Bomo_Chr28 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr28.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr28 -L Bomo_Chr28' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.Bomo_Chr2 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.Bomo_Chr2 --batch-size 5 -L Bomo_Chr2 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.Bomo_Chr2.vcf.gz -V gendb://output.gatk/genomicsdb.Bomo_Chr2 -L Bomo_Chr2' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.pseudochr1 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.pseudochr1 --batch-size 5 -L pseudochr1 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.pseudochr1.vcf.gz -V gendb://output.gatk/genomicsdb.pseudochr1 -L pseudochr1' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.pseudochr2 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.pseudochr2 --batch-size 5 -L pseudochr2 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.pseudochr2.vcf.gz -V gendb://output.gatk/genomicsdb.pseudochr2 -L pseudochr2' + for i in '`cat $ref.fai |cut -f 1`' + '[' -e output.gatk/genomicsdb.pseudochr3 ']' + echo 'singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.pseudochr3 --batch-size 5 -L pseudochr3 --sample-name-map gvcf.list.txt3 --reader-threads 1; singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options \'\''-Xmx25g -XX:ParallelGCThreads=1\'\'' GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.pseudochr3.vcf.gz -V gendb://output.gatk/genomicsdb.pseudochr3 -L pseudochr3' + grep submitted ++ echo /suikou/files/m64g/user2/work/100 ++ sed 's/^[^a-zA-Z]/_/' ++ sed 's/[^a-zA-Z0-9]/_/g' + qsub -hold_jid _suikou_files_m64g_user2_work_100 /suikou/files/m64g/user2/work/100/qsub.sh touch /suikou/files/m64g/user2/work/100/fin + set +x + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 rm -rf output.gatk/genomicsdb.Bomo_Chr1 output.gatk/genomicsdb.Bomo_Chr10 output.gatk/genomicsdb.Bomo_Chr11 output.gatk/genomicsdb.Bomo_Chr12 output.gatk/genomicsdb.Bomo_Chr13 output.gatk/genomicsdb.Bomo_Chr14 output.gatk/genomicsdb.Bomo_Chr15 output.gatk/genomicsdb.Bomo_Chr16 output.gatk/genomicsdb.Bomo_Chr17 output.gatk/genomicsdb.Bomo_Chr18 output.gatk/genomicsdb.Bomo_Chr19 output.gatk/genomicsdb.Bomo_Chr2 output.gatk/genomicsdb.Bomo_Chr20 output.gatk/genomicsdb.Bomo_Chr21 output.gatk/genomicsdb.Bomo_Chr22 output.gatk/genomicsdb.Bomo_Chr23 output.gatk/genomicsdb.Bomo_Chr24 output.gatk/genomicsdb.Bomo_Chr25 output.gatk/genomicsdb.Bomo_Chr26 output.gatk/genomicsdb.Bomo_Chr27 output.gatk/genomicsdb.Bomo_Chr28 output.gatk/genomicsdb.Bomo_Chr3 output.gatk/genomicsdb.Bomo_Chr4 output.gatk/genomicsdb.Bomo_Chr5 output.gatk/genomicsdb.Bomo_Chr6 output.gatk/genomicsdb.Bomo_Chr7 output.gatk/genomicsdb.Bomo_Chr8 output.gatk/genomicsdb.Bomo_Chr9 output.gatk/genomicsdb.pseudochr1 output.gatk/genomicsdb.pseudochr2 output.gatk/genomicsdb.pseudochr3 + grep '^##' + grep -v '^##contig="}' input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.fai pseudochr.txt + grep -v '^##' + awk '-F\t' ' FILENAME==ARGV[1]{chr0[NR]=$1; chr1[NR]=$2; poss[NR]=$3; pose[NR]=$4; n=NR; m=1} FILENAME==ARGV[2]{if(FNR==1){print $0}else{for(i=m;i<=n;i++){m=i; if(chr1[i]==$1 && poss[i]<=$2 && pose[i]>=$2){f=1; break}}; if(f==1){$1=chr0[m]; $2=$2-poss[m]+1; OFS="\t"; print $0; f=0}}} ' pseudochr.txt /dev/stdin ++ head -n 1 pseudochr.re.fa.fai ++ cut -f 1 + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr23.vcf.gz ++ tail -n+2 pseudochr.re.fa.fai ++ cut -f 1 + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr1.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr11.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr5.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr4.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr22.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr15.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr13.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr10.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr12.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr24.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr17.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr9.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr6.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr8.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr18.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr21.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr3.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr19.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + grep -v '^#' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr25.vcf.gz + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr16.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + grep -v '^#' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr7.vcf.gz + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr14.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + grep -v '^#' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr20.vcf.gz + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr26.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr27.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr28.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.Bomo_Chr2.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.pseudochr1.vcf.gz + grep -v '^#' + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + grep -v '^#' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.pseudochr2.vcf.gz + for i in '`tail -n+2 pseudochr.re.fa.fai |cut -f 1`' + singularity exec -B /suikou/files/m64g/user2/work/100:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 zcat output.gatk/out.pseudochr3.vcf.gz + grep -v '^#' ++ onerror 86 ++ status=1 ++ script=WGS~genotyping-by-GATK ++ line=86 ++ shift ++ set +x ------------------------------------------------------------ Error occured on WGS~genotyping-by-GATK [Line 86]: Status 1 PID: 32033 User: user2 Current directory: /suikou/files/m64g/user2/work/100 Command line: WGS~genotyping-by-GATK ------------------------------------------------------------