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 18:30:10.078 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 18:30:11.954 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:11.956 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.0.0 18:30:11.957 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 18:30:11.958 INFO GenomicsDBImport - Executing as user2@m512 on Linux v3.10.0-514.el7.x86_64 amd64 18:30:11.960 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 18:30:11.962 INFO GenomicsDBImport - Start Date/Time: September 17, 2019 6:30:10 PM GMT 18:30:11.963 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:11.964 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:11.967 INFO GenomicsDBImport - HTSJDK Version: 2.18.2 18:30:11.968 INFO GenomicsDBImport - Picard Version: 2.18.25 18:30:11.969 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 18:30:11.970 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 18:30:11.971 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 18:30:11.972 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 18:30:11.973 INFO GenomicsDBImport - Deflater: IntelDeflater 18:30:11.975 INFO GenomicsDBImport - Inflater: IntelInflater 18:30:11.976 INFO GenomicsDBImport - GCS max retries/reopens: 20 18:30:11.977 INFO GenomicsDBImport - Requester pays: disabled 18:30:11.978 INFO GenomicsDBImport - Initializing engine 18:30:12.632 INFO IntervalArgumentCollection - Processing 10017545 bp from intervals 18:30:12.640 INFO GenomicsDBImport - Done initializing engine 18:30:12.940 INFO GenomicsDBImport - Vid Map JSON file will be written to /mnt/output.gatk/genomicsdb.pseudochr2/vidmap.json 18:30:12.941 INFO GenomicsDBImport - Callset Map JSON file will be written to /mnt/output.gatk/genomicsdb.pseudochr2/callset.json 18:30:12.942 INFO GenomicsDBImport - Complete VCF Header will be written to /mnt/output.gatk/genomicsdb.pseudochr2/vcfheader.vcf 18:30:12.943 INFO GenomicsDBImport - Importing to array - /mnt/output.gatk/genomicsdb.pseudochr2/genomicsdb_array 18:30:12.943 INFO ProgressMeter - Starting traversal 18:30:12.945 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 18:30:13.326 INFO GenomicsDBImport - Importing batch 1 with 5 samples 18:30:16.212 INFO GenomicsDBImport - Done importing batch 1/3 18:30:16.501 INFO GenomicsDBImport - Importing batch 2 with 5 samples 18:30:19.159 INFO GenomicsDBImport - Done importing batch 2/3 18:30:19.229 INFO GenomicsDBImport - Importing batch 3 with 2 samples 18:30:21.278 INFO GenomicsDBImport - Done importing batch 3/3 18:30:21.280 INFO ProgressMeter - pseudochr2:1 0.1 3 21.6 18:30:21.282 INFO ProgressMeter - Traversal complete. Processed 3 total batches in 0.1 minutes. 18:30:21.283 INFO GenomicsDBImport - Import of all batches to GenomicsDB completed! 18:30:21.283 INFO GenomicsDBImport - Shutting down engine [September 17, 2019 6:30:21 PM GMT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.19 minutes. Runtime.totalMemory()=2333081600 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.pseudochr2 --batch-size 5 -L pseudochr2 --sample-name-map gvcf.list.txt3 --reader-threads 1 18:30:26.231 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 18:30:28.065 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:28.067 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.0.0 18:30:28.067 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 18:30:28.068 INFO GenotypeGVCFs - Executing as user2@m512 on Linux v3.10.0-514.el7.x86_64 amd64 18:30:28.069 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 18:30:28.070 INFO GenotypeGVCFs - Start Date/Time: September 17, 2019 6:30:26 PM GMT 18:30:28.072 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:28.072 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:28.074 INFO GenotypeGVCFs - HTSJDK Version: 2.18.2 18:30:28.076 INFO GenotypeGVCFs - Picard Version: 2.18.25 18:30:28.077 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 18:30:28.077 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 18:30:28.079 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 18:30:28.079 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 18:30:28.080 INFO GenotypeGVCFs - Deflater: IntelDeflater 18:30:28.081 INFO GenotypeGVCFs - Inflater: IntelInflater 18:30:28.082 INFO GenotypeGVCFs - GCS max retries/reopens: 20 18:30:28.083 INFO GenotypeGVCFs - Requester pays: disabled 18:30:28.084 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 18:30:30.831 INFO IntervalArgumentCollection - Processing 10017545 bp from intervals 18:30:30.845 INFO GenotypeGVCFs - Done initializing engine 18:30:30.936 INFO ProgressMeter - Starting traversal 18:30:30.937 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 18:30:47.057 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.163 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.201 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.222 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.234 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.245 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.251 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.264 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.326 INFO ProgressMeter - pseudochr2:5537776 0.3 1000 3661.2 18:30:47.369 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.438 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.443 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.449 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.528 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.534 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.569 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.573 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.640 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:47.645 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.08067614900000025,Cpu time(s),0.07627047900000007 18:30:47.662 INFO ProgressMeter - pseudochr2:5546581 0.3 4876 17494.5 18:30:47.663 INFO ProgressMeter - Traversal complete. Processed 4876 total variants in 0.3 minutes. 18:30:47.686 INFO GenotypeGVCFs - Shutting down engine [September 17, 2019 6:30:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.36 minutes. Runtime.totalMemory()=2302672896 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.pseudochr2.vcf.gz -V gendb://output.gatk/genomicsdb.pseudochr2 -L pseudochr2