c2997108/biocontainers:gatk-3.8--7 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/picard:2.18.27--0 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/star:2.7.2b--0 using singularity + set -o pipefail ++ find input_1/ ++ egrep '(_R1.*|_1)[.]f(ast|)q$' ++ true + r1= ++ find input_1/ ++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$' + r1gz='input_1/DRR030442_1.fastq.gz input_1/DRR030431_1.fastq.gz input_1/DRR030434_1.fastq.gz input_1/DRR030437_1.fastq.gz input_1/DRR030436_1.fastq.gz input_1/DRR030438_1.fastq.gz input_1/DRR030441_1.fastq.gz input_1/DRR030439_1.fastq.gz input_1/DRR030433_1.fastq.gz input_1/DRR030435_1.fastq.gz input_1/DRR030432_1.fastq.gz input_1/DRR030440_1.fastq.gz' + '[' 'input_1/DRR030442_1.fastq.gz input_1/DRR030431_1.fastq.gz input_1/DRR030434_1.fastq.gz input_1/DRR030437_1.fastq.gz input_1/DRR030436_1.fastq.gz input_1/DRR030438_1.fastq.gz input_1/DRR030441_1.fastq.gz input_1/DRR030439_1.fastq.gz input_1/DRR030433_1.fastq.gz input_1/DRR030435_1.fastq.gz input_1/DRR030432_1.fastq.gz input_1/DRR030440_1.fastq.gz' = '' ']' + r2= ++ for i in '$r1gz' +++ echo input_1/DRR030442_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ echo input_1/DRR030442_1.fastq.gz ++ for i in '$r1gz' +++ echo input_1/DRR030431_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030431_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ echo input_1/DRR030434_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ echo input_1/DRR030434_1.fastq.gz ++ for i in '$r1gz' +++ wc -l +++ echo input_1/DRR030437_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' ++ '[' 1 = 1 ']' ++ echo input_1/DRR030437_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ egrep '_1[.]f(ast|)q[.]gz$' +++ echo input_1/DRR030436_1.fastq.gz +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030436_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ egrep '_1[.]f(ast|)q[.]gz$' +++ echo input_1/DRR030438_1.fastq.gz +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030438_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ echo input_1/DRR030441_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030441_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ egrep '_1[.]f(ast|)q[.]gz$' +++ echo input_1/DRR030439_1.fastq.gz +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030439_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ echo input_1/DRR030433_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030433_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ echo input_1/DRR030435_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030435_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ for i in '$r1gz' +++ egrep '_1[.]f(ast|)q[.]gz$' +++ echo input_1/DRR030432_1.fastq.gz +++ wc -l ++ '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ echo input_1/DRR030432_1.fastq.gz ++ for i in '$r1gz' +++ echo input_1/DRR030440_1.fastq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1/DRR030440_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + r2gz='input_1/DRR030442_2.fastq.gz input_1/DRR030431_2.fastq.gz input_1/DRR030434_2.fastq.gz input_1/DRR030437_2.fastq.gz input_1/DRR030436_2.fastq.gz input_1/DRR030438_2.fastq.gz input_1/DRR030441_2.fastq.gz input_1/DRR030439_2.fastq.gz input_1/DRR030433_2.fastq.gz input_1/DRR030435_2.fastq.gz input_1/DRR030432_2.fastq.gz input_1/DRR030440_2.fastq.gz' + echo '#Check paired-end' #Check paired-end + ls input_1/DRR030442_2.fastq.gz input_1/DRR030431_2.fastq.gz input_1/DRR030434_2.fastq.gz input_1/DRR030437_2.fastq.gz input_1/DRR030436_2.fastq.gz input_1/DRR030438_2.fastq.gz input_1/DRR030441_2.fastq.gz input_1/DRR030439_2.fastq.gz input_1/DRR030433_2.fastq.gz input_1/DRR030435_2.fastq.gz input_1/DRR030432_2.fastq.gz input_1/DRR030440_2.fastq.gz ++ wc -l ++ echo input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa ++ grep '[.]gz$' ++ true + '[' 0 = 1 ']' + ref=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa ++ echo input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa ++ sed 's/[.]\(fa\|fasta\)$//' + refbase=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re + singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa + '[' '!' -e input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.dict ']' + singularity exec -B /suikou/files/m64g/user2/work/101:/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 17:28:12 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 ********** 17:28:12.466 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 17:28:12 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 17:28:12 GMT 2019] Executing as user2@m768 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 17:28:15 GMT 2019] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.06 minutes. Runtime.totalMemory()=536870912 + mkdir -p input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.dir + '[' '' = '' ']' + singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 STAR --runMode genomeGenerate --genomeDir input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa.dir --genomeFastaFiles input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa --runThreadN 8 Sep 18 02:28:16 ..... started STAR run Sep 18 02:28:16 ... starting to generate Genome files WARNING: --genomeSAindexNbases 14 is too large for the genome size=624164864, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 13 Sep 18 02:28:22 Sep 18 02:28:25 ... starting to sort Suffix Array. This may take a long time... Sep 18 02:28:27 ... sorting Suffix Array chunks and saving them to disk... Sep 18 02:31:23 ... loading chunks from disk, packing SA... Sep 18 02:31:34 ... finished generating suffix array Sep 18 02:31:34 ... generating Suffix Array index Sep 18 02:33:09 ... completed Suffix Array index Sep 18 02:33:09 ... writing Genome to disk ... Sep 18 02:33:15 ... writing Suffix Array to disk ... Sep 18 02:33:50 ... writing SAindex to disk Sep 18 02:34:05 ..... finished successfully + mkdir -p output.prinseq + for i in '$r1gz' + grep submitted ++ echo /suikou/files/m64g/user2/work/101 ++ echo input_1/DRR030442_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l ++ sed 's/^[^a-zA-Z]/_/' ++ sed 's/[^a-zA-Z0-9]/_/g' + xargs -I '{}' bash -c 'qsub -N _suikou_files_m64g_user2_work_101 -j y /suikou/files/m64g/user2/work/101/qsubone.sh "{}"' + '[' 1 = 1 ']' ++ echo input_1/DRR030442_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030442_2.fastq.gz ++ basename input_1/DRR030442_1.fastq.gz .gz + i2=DRR030442_1.fastq ++ basename input_1/DRR030442_2.fastq.gz .gz + j2=DRR030442_2.fastq + echo zcat input_1/DRR030442_1.fastq.gz '>' 'DRR030442_1.fastq;' zcat input_1/DRR030442_2.fastq.gz '>' 'DRR030442_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030442_1.fastq -fastq2 DRR030442_2.fastq -out_good output.prinseq/DRR030442_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030442_1.fastq_1.fastq 'output.prinseq/DRR030442_1.fastq;' mv output.prinseq/DRR030442_1.fastq_2.fastq 'output.prinseq/DRR030442_2.fastq;rm' -f DRR030442_1.fastq DRR030442_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030431_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ echo input_1/DRR030431_1.fastq.gz + j=input_1/DRR030431_2.fastq.gz ++ basename input_1/DRR030431_1.fastq.gz .gz + i2=DRR030431_1.fastq ++ basename input_1/DRR030431_2.fastq.gz .gz + j2=DRR030431_2.fastq + echo zcat input_1/DRR030431_1.fastq.gz '>' 'DRR030431_1.fastq;' zcat input_1/DRR030431_2.fastq.gz '>' 'DRR030431_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030431_1.fastq -fastq2 DRR030431_2.fastq -out_good output.prinseq/DRR030431_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030431_1.fastq_1.fastq 'output.prinseq/DRR030431_1.fastq;' mv output.prinseq/DRR030431_1.fastq_2.fastq 'output.prinseq/DRR030431_2.fastq;rm' -f DRR030431_1.fastq DRR030431_2.fastq + for i in '$r1gz' ++ egrep '_1[.]f(ast|)q[.]gz$' ++ echo input_1/DRR030434_1.fastq.gz ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030434_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030434_2.fastq.gz ++ basename input_1/DRR030434_1.fastq.gz .gz + i2=DRR030434_1.fastq ++ basename input_1/DRR030434_2.fastq.gz .gz + j2=DRR030434_2.fastq + echo zcat input_1/DRR030434_1.fastq.gz '>' 'DRR030434_1.fastq;' zcat input_1/DRR030434_2.fastq.gz '>' 'DRR030434_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030434_1.fastq -fastq2 DRR030434_2.fastq -out_good output.prinseq/DRR030434_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030434_1.fastq_1.fastq 'output.prinseq/DRR030434_1.fastq;' mv output.prinseq/DRR030434_1.fastq_2.fastq 'output.prinseq/DRR030434_2.fastq;rm' -f DRR030434_1.fastq DRR030434_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030437_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030437_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030437_2.fastq.gz ++ basename input_1/DRR030437_1.fastq.gz .gz + i2=DRR030437_1.fastq ++ basename input_1/DRR030437_2.fastq.gz .gz + j2=DRR030437_2.fastq + echo zcat input_1/DRR030437_1.fastq.gz '>' 'DRR030437_1.fastq;' zcat input_1/DRR030437_2.fastq.gz '>' 'DRR030437_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030437_1.fastq -fastq2 DRR030437_2.fastq -out_good output.prinseq/DRR030437_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030437_1.fastq_1.fastq 'output.prinseq/DRR030437_1.fastq;' mv output.prinseq/DRR030437_1.fastq_2.fastq 'output.prinseq/DRR030437_2.fastq;rm' -f DRR030437_1.fastq DRR030437_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030436_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030436_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030436_2.fastq.gz ++ basename input_1/DRR030436_1.fastq.gz .gz + i2=DRR030436_1.fastq ++ basename input_1/DRR030436_2.fastq.gz .gz + j2=DRR030436_2.fastq + echo zcat input_1/DRR030436_1.fastq.gz '>' 'DRR030436_1.fastq;' zcat input_1/DRR030436_2.fastq.gz '>' 'DRR030436_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030436_1.fastq -fastq2 DRR030436_2.fastq -out_good output.prinseq/DRR030436_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030436_1.fastq_1.fastq 'output.prinseq/DRR030436_1.fastq;' mv output.prinseq/DRR030436_1.fastq_2.fastq 'output.prinseq/DRR030436_2.fastq;rm' -f DRR030436_1.fastq DRR030436_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030438_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030438_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030438_2.fastq.gz ++ basename input_1/DRR030438_1.fastq.gz .gz + i2=DRR030438_1.fastq ++ basename input_1/DRR030438_2.fastq.gz .gz + j2=DRR030438_2.fastq + echo zcat input_1/DRR030438_1.fastq.gz '>' 'DRR030438_1.fastq;' zcat input_1/DRR030438_2.fastq.gz '>' 'DRR030438_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030438_1.fastq -fastq2 DRR030438_2.fastq -out_good output.prinseq/DRR030438_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030438_1.fastq_1.fastq 'output.prinseq/DRR030438_1.fastq;' mv output.prinseq/DRR030438_1.fastq_2.fastq 'output.prinseq/DRR030438_2.fastq;rm' -f DRR030438_1.fastq DRR030438_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030441_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030441_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030441_2.fastq.gz ++ basename input_1/DRR030441_1.fastq.gz .gz + i2=DRR030441_1.fastq ++ basename input_1/DRR030441_2.fastq.gz .gz + j2=DRR030441_2.fastq + echo zcat input_1/DRR030441_1.fastq.gz '>' 'DRR030441_1.fastq;' zcat input_1/DRR030441_2.fastq.gz '>' 'DRR030441_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030441_1.fastq -fastq2 DRR030441_2.fastq -out_good output.prinseq/DRR030441_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030441_1.fastq_1.fastq 'output.prinseq/DRR030441_1.fastq;' mv output.prinseq/DRR030441_1.fastq_2.fastq 'output.prinseq/DRR030441_2.fastq;rm' -f DRR030441_1.fastq DRR030441_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030439_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ echo input_1/DRR030439_1.fastq.gz + j=input_1/DRR030439_2.fastq.gz ++ basename input_1/DRR030439_1.fastq.gz .gz + i2=DRR030439_1.fastq ++ basename input_1/DRR030439_2.fastq.gz .gz + j2=DRR030439_2.fastq + echo zcat input_1/DRR030439_1.fastq.gz '>' 'DRR030439_1.fastq;' zcat input_1/DRR030439_2.fastq.gz '>' 'DRR030439_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030439_1.fastq -fastq2 DRR030439_2.fastq -out_good output.prinseq/DRR030439_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030439_1.fastq_1.fastq 'output.prinseq/DRR030439_1.fastq;' mv output.prinseq/DRR030439_1.fastq_2.fastq 'output.prinseq/DRR030439_2.fastq;rm' -f DRR030439_1.fastq DRR030439_2.fastq + for i in '$r1gz' ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l ++ echo input_1/DRR030433_1.fastq.gz + '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' ++ echo input_1/DRR030433_1.fastq.gz + j=input_1/DRR030433_2.fastq.gz ++ basename input_1/DRR030433_1.fastq.gz .gz + i2=DRR030433_1.fastq ++ basename input_1/DRR030433_2.fastq.gz .gz + j2=DRR030433_2.fastq + echo zcat input_1/DRR030433_1.fastq.gz '>' 'DRR030433_1.fastq;' zcat input_1/DRR030433_2.fastq.gz '>' 'DRR030433_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030433_1.fastq -fastq2 DRR030433_2.fastq -out_good output.prinseq/DRR030433_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030433_1.fastq_1.fastq 'output.prinseq/DRR030433_1.fastq;' mv output.prinseq/DRR030433_1.fastq_2.fastq 'output.prinseq/DRR030433_2.fastq;rm' -f DRR030433_1.fastq DRR030433_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030435_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030435_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030435_2.fastq.gz ++ basename input_1/DRR030435_1.fastq.gz .gz + i2=DRR030435_1.fastq ++ basename input_1/DRR030435_2.fastq.gz .gz + j2=DRR030435_2.fastq + echo zcat input_1/DRR030435_1.fastq.gz '>' 'DRR030435_1.fastq;' zcat input_1/DRR030435_2.fastq.gz '>' 'DRR030435_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030435_1.fastq -fastq2 DRR030435_2.fastq -out_good output.prinseq/DRR030435_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030435_1.fastq_1.fastq 'output.prinseq/DRR030435_1.fastq;' mv output.prinseq/DRR030435_1.fastq_2.fastq 'output.prinseq/DRR030435_2.fastq;rm' -f DRR030435_1.fastq DRR030435_2.fastq + for i in '$r1gz' ++ egrep '_1[.]f(ast|)q[.]gz$' ++ echo input_1/DRR030432_1.fastq.gz ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030432_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030432_2.fastq.gz ++ basename input_1/DRR030432_1.fastq.gz .gz + i2=DRR030432_1.fastq ++ basename input_1/DRR030432_2.fastq.gz .gz + j2=DRR030432_2.fastq + echo zcat input_1/DRR030432_1.fastq.gz '>' 'DRR030432_1.fastq;' zcat input_1/DRR030432_2.fastq.gz '>' 'DRR030432_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030432_1.fastq -fastq2 DRR030432_2.fastq -out_good output.prinseq/DRR030432_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030432_1.fastq_1.fastq 'output.prinseq/DRR030432_1.fastq;' mv output.prinseq/DRR030432_1.fastq_2.fastq 'output.prinseq/DRR030432_2.fastq;rm' -f DRR030432_1.fastq DRR030432_2.fastq + for i in '$r1gz' ++ echo input_1/DRR030440_1.fastq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1/DRR030440_1.fastq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1/DRR030440_2.fastq.gz ++ basename input_1/DRR030440_1.fastq.gz .gz + i2=DRR030440_1.fastq ++ basename input_1/DRR030440_2.fastq.gz .gz + j2=DRR030440_2.fastq + echo zcat input_1/DRR030440_1.fastq.gz '>' 'DRR030440_1.fastq;' zcat input_1/DRR030440_2.fastq.gz '>' 'DRR030440_2.fastq;' singularity exec -B /suikou/files/m64g/user2/work/101:/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 prinseq-lite.pl -fastq DRR030440_1.fastq -fastq2 DRR030440_2.fastq -out_good output.prinseq/DRR030440_1.fastq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window '5;' mv output.prinseq/DRR030440_1.fastq_1.fastq 'output.prinseq/DRR030440_1.fastq;' mv output.prinseq/DRR030440_1.fastq_2.fastq 'output.prinseq/DRR030440_2.fastq;rm' -f DRR030440_1.fastq DRR030440_2.fastq + grep submitted ++ echo /suikou/files/m64g/user2/work/101 ++ sed 's/^[^a-zA-Z]/_/' ++ sed 's/[^a-zA-Z0-9]/_/g' + qsub -hold_jid _suikou_files_m64g_user2_work_101 /suikou/files/m64g/user2/work/101/qsubone.sh touch /suikou/files/m64g/user2/work/101/fin + set +x + rm -f output.prinseq/DRR030431_1.fastq_1_singletons.fastq output.prinseq/DRR030431_1.fastq_2_singletons.fastq output.prinseq/DRR030432_1.fastq_1_singletons.fastq output.prinseq/DRR030432_1.fastq_2_singletons.fastq output.prinseq/DRR030433_1.fastq_1_singletons.fastq output.prinseq/DRR030433_1.fastq_2_singletons.fastq output.prinseq/DRR030434_1.fastq_1_singletons.fastq output.prinseq/DRR030434_1.fastq_2_singletons.fastq output.prinseq/DRR030435_1.fastq_1_singletons.fastq output.prinseq/DRR030435_1.fastq_2_singletons.fastq output.prinseq/DRR030436_1.fastq_1_singletons.fastq output.prinseq/DRR030436_1.fastq_2_singletons.fastq output.prinseq/DRR030437_1.fastq_1_singletons.fastq output.prinseq/DRR030437_1.fastq_2_singletons.fastq output.prinseq/DRR030438_1.fastq_1_singletons.fastq output.prinseq/DRR030438_1.fastq_2_singletons.fastq output.prinseq/DRR030439_1.fastq_1_singletons.fastq output.prinseq/DRR030439_1.fastq_2_singletons.fastq output.prinseq/DRR030440_1.fastq_1_singletons.fastq output.prinseq/DRR030440_1.fastq_2_singletons.fastq output.prinseq/DRR030441_1.fastq_1_singletons.fastq output.prinseq/DRR030441_1.fastq_2_singletons.fastq output.prinseq/DRR030442_1.fastq_1_singletons.fastq output.prinseq/DRR030442_1.fastq_2_singletons.fastq ++ find output.prinseq/ ++ egrep '(_R1.*|_1)[.]f(ast|)q$' + r1='output.prinseq/DRR030433_1.fastq output.prinseq/DRR030441_1.fastq output.prinseq/DRR030438_1.fastq output.prinseq/DRR030435_1.fastq output.prinseq/DRR030442_1.fastq output.prinseq/DRR030436_1.fastq output.prinseq/DRR030431_1.fastq output.prinseq/DRR030432_1.fastq output.prinseq/DRR030440_1.fastq output.prinseq/DRR030434_1.fastq output.prinseq/DRR030439_1.fastq output.prinseq/DRR030437_1.fastq' + cat + cat + cat + cat + mkdir -p output.STAR + for i in '$r1' + grep submitted ++ echo /suikou/files/m64g/user2/work/101 ++ echo output.prinseq/DRR030433_1.fastq ++ sed 's/[^a-zA-Z0-9]/_/g' ++ egrep '_1[.]f(ast|)q$' ++ wc -l ++ sed 's/^[^a-zA-Z]/_/' + xargs -I '{}' bash -c 'qsub -N _suikou_files_m64g_user2_work_101 -j y /suikou/files/m64g/user2/work/101/qsub.sh "{}"' + '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' ++ echo output.prinseq/DRR030433_1.fastq + j=output.prinseq/DRR030433_2.fastq +++ echo output.prinseq/DRR030433_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030433 + outbase=DRR030433 + '[' '' = '' ']' ++ basename output.prinseq/DRR030433_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030433_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030433_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030433_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030433_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030441_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030441_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030441_2.fastq +++ echo output.prinseq/DRR030441_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030441 + outbase=DRR030441 + '[' '' = '' ']' ++ basename output.prinseq/DRR030441_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030441_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030441_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030441_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030441_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030438_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030438_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030438_2.fastq +++ echo output.prinseq/DRR030438_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030438 + outbase=DRR030438 + '[' '' = '' ']' ++ basename output.prinseq/DRR030438_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030438_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030438_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030438_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030438_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030435_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030435_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030435_2.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' +++ echo output.prinseq/DRR030435_1.fastq ++ basename output.prinseq/DRR030435 + outbase=DRR030435 + '[' '' = '' ']' ++ basename output.prinseq/DRR030435_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030435_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030435_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030435_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030435_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030442_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030442_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030442_2.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' +++ echo output.prinseq/DRR030442_1.fastq ++ basename output.prinseq/DRR030442 + outbase=DRR030442 + '[' '' = '' ']' ++ basename output.prinseq/DRR030442_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030442_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030442_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030442_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030442_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030436_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030436_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030436_2.fastq +++ echo output.prinseq/DRR030436_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030436 + outbase=DRR030436 + '[' '' = '' ']' ++ basename output.prinseq/DRR030436_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030436_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030436_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030436_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030436_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030431_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030431_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030431_2.fastq +++ echo output.prinseq/DRR030431_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030431 + outbase=DRR030431 + '[' '' = '' ']' ++ basename output.prinseq/DRR030431_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030431_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030431_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030431_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030431_1.fastq 2>&1' + for i in '$r1' ++ egrep '_1[.]f(ast|)q$' ++ echo output.prinseq/DRR030432_1.fastq ++ wc -l + '[' 1 = 1 ']' ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' ++ echo output.prinseq/DRR030432_1.fastq + j=output.prinseq/DRR030432_2.fastq +++ echo output.prinseq/DRR030432_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030432 + outbase=DRR030432 + '[' '' = '' ']' ++ basename output.prinseq/DRR030432_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030432_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030432_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030432_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030432_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030440_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030440_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030440_2.fastq +++ echo output.prinseq/DRR030440_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030440 + outbase=DRR030440 + '[' '' = '' ']' ++ basename output.prinseq/DRR030440_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030440_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030440_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030440_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030440_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030434_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030434_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030434_2.fastq +++ echo output.prinseq/DRR030434_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030434 + outbase=DRR030434 + '[' '' = '' ']' ++ basename output.prinseq/DRR030434_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030434_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030434_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030434_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030434_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030439_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030439_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030439_2.fastq +++ echo output.prinseq/DRR030439_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030439 + outbase=DRR030439 + '[' '' = '' ']' ++ basename output.prinseq/DRR030439_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030439_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030439_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030439_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030439_1.fastq 2>&1' + for i in '$r1' ++ echo output.prinseq/DRR030437_1.fastq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/DRR030437_1.fastq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/DRR030437_2.fastq +++ echo output.prinseq/DRR030437_1.fastq +++ sed 's/_1[.]f\(ast\|\)q\(\|.gz\)$//' ++ basename output.prinseq/DRR030437 + outbase=DRR030437 + '[' '' = '' ']' ++ basename output.prinseq/DRR030437_1.fastq + echo '(singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/star:2.7.2b--0 bash ./run-STAR.sh output.prinseq/DRR030437_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/picard:2.18.27--0 bash ./run-picard.sh output.prinseq/DRR030437_1.fastq 8 52428 && singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 bash ./run-GATK.sh output.prinseq/DRR030437_1.fastq input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa 8 52428) > log.DRR030437_1.fastq 2>&1' + grep submitted ++ echo /suikou/files/m64g/user2/work/101 ++ sed 's/^[^a-zA-Z]/_/' ++ sed 's/[^a-zA-Z0-9]/_/g' + qsub -hold_jid _suikou_files_m64g_user2_work_101 /suikou/files/m64g/user2/work/101/qsub.sh touch /suikou/files/m64g/user2/work/101/fin + set +x + I= + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam -I output.STAR/DRR030438.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam -I output.STAR/DRR030438.bam -I output.STAR/DRR030439.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam -I output.STAR/DRR030438.bam -I output.STAR/DRR030439.bam -I output.STAR/DRR030440.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam -I output.STAR/DRR030438.bam -I output.STAR/DRR030439.bam -I output.STAR/DRR030440.bam -I output.STAR/DRR030441.bam' + for i in 'output.STAR/*.bam' + I=' -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam -I output.STAR/DRR030438.bam -I output.STAR/DRR030439.bam -I output.STAR/DRR030440.bam -I output.STAR/DRR030441.bam -I output.STAR/DRR030442.bam' + singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/c2997108/biocontainers:gatk-3.8--7 gatk3 -Xmx52428M -T HaplotypeCaller -R input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam -I output.STAR/DRR030438.bam -I output.STAR/DRR030439.bam -I output.STAR/DRR030440.bam -I output.STAR/DRR030441.bam -I output.STAR/DRR030442.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -o output.vcf -nct 8 INFO 18:11:14,169 HelpFormatter - ---------------------------------------------------------------------------------- INFO 18:11:14,171 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 INFO 18:11:14,172 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 18:11:14,172 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 18:11:14,173 HelpFormatter - [Tue Sep 17 18:11:14 GMT 2019] Executing on Linux 3.10.0-514.el7.x86_64 amd64 INFO 18:11:14,173 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_192-b01 INFO 18:11:14,176 HelpFormatter - Program Args: -T HaplotypeCaller -R input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa -I output.STAR/DRR030431.bam -I output.STAR/DRR030432.bam -I output.STAR/DRR030433.bam -I output.STAR/DRR030434.bam -I output.STAR/DRR030435.bam -I output.STAR/DRR030436.bam -I output.STAR/DRR030437.bam -I output.STAR/DRR030438.bam -I output.STAR/DRR030439.bam -I output.STAR/DRR030440.bam -I output.STAR/DRR030441.bam -I output.STAR/DRR030442.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -o output.vcf -nct 8 INFO 18:11:14,181 HelpFormatter - Executing as user2@m768 on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_192-b01. INFO 18:11:14,182 HelpFormatter - Date/Time: 2019/09/17 18:11:14 INFO 18:11:14,183 HelpFormatter - ---------------------------------------------------------------------------------- INFO 18:11:14,183 HelpFormatter - ---------------------------------------------------------------------------------- ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/usr/local/opt/gatk-3.8/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console... INFO 18:11:14,286 GenomeAnalysisEngine - Deflater: IntelDeflater INFO 18:11:14,287 GenomeAnalysisEngine - Inflater: IntelInflater INFO 18:11:14,287 GenomeAnalysisEngine - Strictness is SILENT INFO 18:11:14,483 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500 INFO 18:11:14,488 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 18:11:15,054 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.56 INFO 18:11:15,182 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 18:11:15,196 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 16 processors available on this machine INFO 18:11:15,316 GenomeAnalysisEngine - Preparing for traversal over 12 BAM files INFO 18:11:15,440 GenomeAnalysisEngine - Done preparing for traversal INFO 18:11:15,440 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 18:11:15,441 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 18:11:15,442 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime INFO 18:11:15,442 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output INFO 18:11:15,473 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. INFO 18:11:15,474 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. INFO 18:11:15,537 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 18:11:15,538 PairHMM - Performance profiling for PairHMM is disabled because the program is being run with multiple threads (-nct>1) option Profiling is enabled only when running in single thread mode INFO 18:11:16,447 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads WARN 18:11:16,478 AnnotationUtils - Annotation will not be calculated, genotype is not called WARN 18:11:16,519 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not HaplotypeCaller INFO 18:11:16,901 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:11:16,926 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:11:16,957 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:11:16,994 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:11:17,023 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:11:17,236 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:11:17,642 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:11:45,444 ProgressMeter - Bomo_Chr3:1577258 2.9062732E7 30.0 s 1.0 s 6.7% 7.5 m 7.0 m INFO 18:12:15,446 ProgressMeter - Bomo_Chr4:13021315 4.4275685E7 60.0 s 1.0 s 12.4% 8.0 m 7.0 m INFO 18:12:45,454 ProgressMeter - Bomo_Chr6:3733410 8.2074898E7 90.0 s 1.0 s 18.6% 8.0 m 6.5 m INFO 18:13:15,456 ProgressMeter - Bomo_Chr8:9870187 1.12670396E8 120.0 s 1.0 s 26.6% 7.5 m 5.5 m INFO 18:13:45,457 ProgressMeter - Bomo_Chr10:7867766 1.45728685E8 2.5 m 1.0 s 33.4% 7.5 m 5.0 m INFO 18:14:15,458 ProgressMeter - Bomo_Chr11:13259022 1.63343456E8 3.0 m 1.0 s 38.4% 7.8 m 4.8 m INFO 18:14:45,460 ProgressMeter - Bomo_Chr13:9787477 2.01364071E8 3.5 m 1.0 s 45.9% 7.6 m 4.1 m INFO 18:15:15,462 ProgressMeter - Bomo_Chr15:9539608 2.3244467E8 4.0 m 1.0 s 52.6% 7.6 m 3.6 m INFO 18:15:45,463 ProgressMeter - Bomo_Chr17:5051700 2.65222254E8 4.5 m 1.0 s 58.7% 7.7 m 3.2 m INFO 18:16:15,466 ProgressMeter - Bomo_Chr19:4705517 2.97761979E8 5.0 m 1.0 s 65.7% 7.6 m 2.6 m INFO 18:16:45,468 ProgressMeter - Bomo_Chr21:9746045 3.24933999E8 5.5 m 1.0 s 72.7% 7.6 m 2.1 m INFO 18:17:15,469 ProgressMeter - Bomo_Chr23:12045643 3.58726917E8 6.0 m 1.0 s 80.6% 7.4 m 86.0 s INFO 18:17:45,471 ProgressMeter - Bomo_Chr24:17330310 3.80192609E8 6.5 m 1.0 s 86.4% 7.5 m 61.0 s INFO 18:18:15,473 ProgressMeter - Bomo_Chr26:11455027 4.12100679E8 7.0 m 1.0 s 92.0% 7.6 m 36.0 s INFO 18:18:45,475 ProgressMeter - Bomo_Scaf456:14269 4.57635607E8 7.5 m 0.0 s 99.4% 7.5 m 2.0 s INFO 18:18:59,704 VectorLoglessPairHMM - Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation [INFO] Available threads: 16 [INFO] Requested threads: 1 [INFO] Using 1 threads INFO 18:18:59,706 HaplotypeCaller - Ran local assembly on 40359 active regions INFO 18:18:59,815 ProgressMeter - done 4.6028209E8 7.7 m 1.0 s 100.0% 7.7 m 0.0 s INFO 18:18:59,816 ProgressMeter - Total runtime 464.38 secs, 7.74 min, 0.13 hours INFO 18:18:59,816 MicroScheduler - 264636 reads were filtered out during the traversal out of approximately 2766819 total reads (9.56%) INFO 18:18:59,817 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter INFO 18:18:59,817 MicroScheduler - -> 15894 reads (0.57% of total) failing DuplicateReadFilter INFO 18:18:59,817 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 18:18:59,818 MicroScheduler - -> 248742 reads (8.99% of total) failing HCMappingQualityFilter INFO 18:18:59,818 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 18:18:59,819 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 18:18:59,819 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter INFO 18:18:59,820 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter ------------------------------------------------------------------------------------------ Done. There were 2 WARN messages, the first 2 are repeated below. WARN 18:11:16,478 AnnotationUtils - Annotation will not be calculated, genotype is not called WARN 18:11:16,519 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not HaplotypeCaller ------------------------------------------------------------------------------------------ + cat output.vcf + grep -v '^##' + sed 's/\t$//' + awk '-F\t' ' {ORS="\t"; print $1"\t"$2"\t"$4"\t"$5"\t"$6"\t"$8; for(i=10;i<=NF;i++){split($i,arr,":"); if(NR==1){print $i}else{if(arr[4]>=10){print arr[1]}else{print "./."}}}; ORS="\n"; print "" + awk '-F\t' '{n=0;for(i=7;i<=NF;i++){if($i=="./."){n++}}; if(n1{ORS="\t"; print $1":"$2":"$3":"$4; for(i=7;i<=NF;i++){split($i,arr2,"/"); if(arr2[1]>1){arr2[1]=1}; if(arr2[2]>1){arr2[2]=1}; print arr2[1]+arr2[2]}; ORS="\n"; print ""} ' + cut -f 2- output.nonNA.txt ++ head -n 1 output.tsv ++ awk '-F\t' '{if((NF-6)/10<8){print 8}else{print (NF-6)/10}}' + w=8 ++ head -n 1 output.tsv ++ awk '-F\t' '{if((NF-6)/10<8){print 4}else{print (NF-6)/20}}' + h=4 + echo 'a=read.table('\''output.nonNA.tsv'\'',sep='\''\t'\'',header=T) c=cor(a); for(i in 1:ncol(c)){c[is.na(c[,i]),i]=0}; result=hclust(as.dist(1-c),'\''ave'\'') pdf('\''sample-relation.pdf'\'',width=8, height=4, pointsize=2) plot(result) dev.off()' + singularity exec -B /suikou/files/m64g/user2/work/101:/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 R --vanilla R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_COLLATE failed, using "C" 3: Setting LC_TIME failed, using "C" 4: Setting LC_MESSAGES failed, using "C" 5: Setting LC_MONETARY failed, using "C" 6: Setting LC_PAPER failed, using "C" 7: Setting LC_MEASUREMENT failed, using "C" > a=read.table('output.nonNA.tsv',sep='\t',header=T) > c=cor(a); for(i in 1:ncol(c)){c[is.na(c[,i]),i]=0}; result=hclust(as.dist(1-c),'ave') > pdf('sample-relation.pdf',width=8, height=4, pointsize=2) > plot(result) > dev.off() null device 1 > + post_processing + '[' 1 = 1 ']' + '[' 'singularity exec -B /suikou/files/m64g/user2/work/101:/mnt --pwd /mnt /home/user2/img/' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']' + echo 0 + exit