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/gatk4:4.1.0.0--0 quay.io/biocontainers/picard:2.18.27--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/yoshitake/121:/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) INFO 2019-09-24 16:01:59 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 ********** 16:02:00.278 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 24 16:02:00 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 24 16:02:02 GMT 2019] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=536870912 + singularity exec -B /suikou/files/m64g/user2/work/yoshitake/121:/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 + ref=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa + I= + for i in '"$input_1"/*.bam' + I='-I input_1/SRR4425244.bam' + for i in '"$input_1"/*.bam' + I='-I input_1/SRR4425245.bam' + singularity exec -B /suikou/files/m64g/user2/work/yoshitake/121:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/gatk4:4.1.0.0--0 gatk --java-options -Xmx25g HaplotypeCaller -L Bomo_Chr1 -I input_1/SRR4425245.bam -R input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa -O output.vcf 16:02:10.868 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:02:12.546 INFO HaplotypeCaller - ------------------------------------------------------------ 16:02:13.162 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.0.0 16:02:13.162 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:02:13.163 INFO HaplotypeCaller - Initializing engine 16:02:13.596 INFO IntervalArgumentCollection - Processing 20666287 bp from intervals 16:02:13.604 INFO HaplotypeCaller - Done initializing engine 16:02:13.623 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output 16:02:13.635 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/local/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 16:02:13.645 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/usr/local/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 16:02:13.690 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 16:02:13.691 INFO IntelPairHmm - Available threads: 20 16:02:13.691 INFO IntelPairHmm - Requested threads: 4 16:02:13.691 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 16:02:13.729 INFO ProgressMeter - Starting traversal 16:02:13.729 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 16:02:23.729 INFO ProgressMeter - Bomo_Chr1:16919484 0.2 57660 345960.0 16:02:24.941 INFO HaplotypeCaller - 138 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter) 138 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) 138 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) 138 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) 138 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) 138 read(s) filtered by: (((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) 138 read(s) filtered by: ((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) 138 read(s) filtered by: (MappingQualityReadFilter AND MappingQualityAvailableReadFilter) 138 read(s) filtered by: MappingQualityReadFilter 16:02:24.941 INFO ProgressMeter - Bomo_Chr1:20665931 0.2 70351 376477.0 16:02:24.941 INFO ProgressMeter - Traversal complete. Processed 70351 total regions in 0.2 minutes. 16:02:24.960 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004140947 16:02:24.960 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.457220781 16:02:24.960 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.19 sec 16:02:24.960 INFO HaplotypeCaller - Shutting down engine [September 24, 2019 4:02:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.24 minutes. Runtime.totalMemory()=2896691200 Using GATK jar /usr/local/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx25g -jar /usr/local/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar HaplotypeCaller -L Bomo_Chr1 -I input_1/SRR4425245.bam -R input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa -O output.vcf + post_processing + '[' 1 = 1 ']' + '[' 'singularity exec -B /suikou/files/m64g/user2/work/yoshitake/121:/mnt --pwd /mnt /home/user2/img/' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']' + echo 0 + exit