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 18:30:11.177 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 18:30:13.149 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:13.152 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.0.0 18:30:13.153 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 18:30:13.154 INFO GenomicsDBImport - Executing as user2@m256 on Linux v3.10.0-514.el7.x86_64 amd64 18:30:13.155 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 18:30:13.156 INFO GenomicsDBImport - Start Date/Time: September 17, 2019 6:30:11 PM GMT 18:30:13.157 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:13.157 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:13.159 INFO GenomicsDBImport - HTSJDK Version: 2.18.2 18:30:13.160 INFO GenomicsDBImport - Picard Version: 2.18.25 18:30:13.161 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 18:30:13.162 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 18:30:13.162 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 18:30:13.163 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 18:30:13.164 INFO GenomicsDBImport - Deflater: IntelDeflater 18:30:13.165 INFO GenomicsDBImport - Inflater: IntelInflater 18:30:13.165 INFO GenomicsDBImport - GCS max retries/reopens: 20 18:30:13.166 INFO GenomicsDBImport - Requester pays: disabled 18:30:13.167 INFO GenomicsDBImport - Initializing engine 18:30:13.733 INFO IntervalArgumentCollection - Processing 1780151 bp from intervals 18:30:13.744 INFO GenomicsDBImport - Done initializing engine 18:30:14.052 INFO GenomicsDBImport - Vid Map JSON file will be written to /mnt/output.gatk/genomicsdb.pseudochr3/vidmap.json 18:30:14.053 INFO GenomicsDBImport - Callset Map JSON file will be written to /mnt/output.gatk/genomicsdb.pseudochr3/callset.json 18:30:14.054 INFO GenomicsDBImport - Complete VCF Header will be written to /mnt/output.gatk/genomicsdb.pseudochr3/vcfheader.vcf 18:30:14.055 INFO GenomicsDBImport - Importing to array - /mnt/output.gatk/genomicsdb.pseudochr3/genomicsdb_array 18:30:14.056 INFO ProgressMeter - Starting traversal 18:30:14.057 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 18:30:14.588 INFO GenomicsDBImport - Importing batch 1 with 5 samples 18:30:16.212 INFO GenomicsDBImport - Done importing batch 1/3 18:30:16.444 INFO GenomicsDBImport - Importing batch 2 with 5 samples 18:30:17.849 INFO GenomicsDBImport - Done importing batch 2/3 18:30:18.086 INFO GenomicsDBImport - Importing batch 3 with 2 samples 18:30:19.532 INFO GenomicsDBImport - Done importing batch 3/3 18:30:19.537 INFO ProgressMeter - pseudochr3:1 0.1 3 32.9 18:30:19.539 INFO ProgressMeter - Traversal complete. Processed 3 total batches in 0.1 minutes. 18:30:19.540 INFO GenomicsDBImport - Import of all batches to GenomicsDB completed! 18:30:19.541 INFO GenomicsDBImport - Shutting down engine [September 17, 2019 6:30:19 PM GMT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=2327314432 Tool returned: true 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 -XX:ParallelGCThreads=1 -jar /usr/local/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar GenomicsDBImport --genomicsdb-workspace-path output.gatk/genomicsdb.pseudochr3 --batch-size 5 -L pseudochr3 --sample-name-map gvcf.list.txt3 --reader-threads 1 18:30:25.460 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 18:30:27.477 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:27.479 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.0.0 18:30:27.480 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 18:30:27.481 INFO GenotypeGVCFs - Executing as user2@m256 on Linux v3.10.0-514.el7.x86_64 amd64 18:30:27.482 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 18:30:27.483 INFO GenotypeGVCFs - Start Date/Time: September 17, 2019 6:30:25 PM GMT 18:30:27.484 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:27.485 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:27.487 INFO GenotypeGVCFs - HTSJDK Version: 2.18.2 18:30:27.487 INFO GenotypeGVCFs - Picard Version: 2.18.25 18:30:27.488 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 18:30:27.489 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 18:30:27.490 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 18:30:27.491 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 18:30:27.492 INFO GenotypeGVCFs - Deflater: IntelDeflater 18:30:27.493 INFO GenotypeGVCFs - Inflater: IntelInflater 18:30:27.494 INFO GenotypeGVCFs - GCS max retries/reopens: 20 18:30:27.495 INFO GenotypeGVCFs - Requester pays: disabled 18:30:27.495 INFO GenotypeGVCFs - Initializing engine WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records 18:30:30.463 INFO IntervalArgumentCollection - Processing 1780151 bp from intervals 18:30:30.480 INFO GenotypeGVCFs - Done initializing engine 18:30:30.586 INFO ProgressMeter - Starting traversal 18:30:30.587 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.03115915099999999,Cpu time(s),0.029413371 18:30:33.826 INFO ProgressMeter - unmapped 0.1 47 871.7 18:30:33.827 INFO ProgressMeter - Traversal complete. Processed 47 total variants in 0.1 minutes. 18:30:33.851 INFO GenotypeGVCFs - Shutting down engine [September 17, 2019 6:30:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=2293235712 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 -XX:ParallelGCThreads=1 -jar /usr/local/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar GenotypeGVCFs -R pseudochr.re.fa -O output.gatk/out.pseudochr3.vcf.gz -V gendb://output.gatk/genomicsdb.pseudochr3 -L pseudochr3