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 18:30:11.347 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 18:30:13.286 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:13.288 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.0.0 18:30:13.289 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 18:30:13.290 INFO GenomicsDBImport - Executing as user2@m256 on Linux v3.10.0-514.el7.x86_64 amd64 18:30:13.291 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 18:30:13.293 INFO GenomicsDBImport - Start Date/Time: September 17, 2019 6:30:11 PM GMT 18:30:13.294 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:13.295 INFO GenomicsDBImport - ------------------------------------------------------------ 18:30:13.297 INFO GenomicsDBImport - HTSJDK Version: 2.18.2 18:30:13.298 INFO GenomicsDBImport - Picard Version: 2.18.25 18:30:13.299 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 18:30:13.300 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 18:30:13.301 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 18:30:13.302 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 18:30:13.303 INFO GenomicsDBImport - Deflater: IntelDeflater 18:30:13.303 INFO GenomicsDBImport - Inflater: IntelInflater 18:30:13.304 INFO GenomicsDBImport - GCS max retries/reopens: 20 18:30:13.305 INFO GenomicsDBImport - Requester pays: disabled 18:30:13.306 INFO GenomicsDBImport - Initializing engine 18:30:13.915 INFO IntervalArgumentCollection - Processing 10010372 bp from intervals 18:30:13.919 INFO GenomicsDBImport - Done initializing engine 18:30:14.198 INFO GenomicsDBImport - Vid Map JSON file will be written to /mnt/output.gatk/genomicsdb.pseudochr1/vidmap.json 18:30:14.199 INFO GenomicsDBImport - Callset Map JSON file will be written to /mnt/output.gatk/genomicsdb.pseudochr1/callset.json 18:30:14.200 INFO GenomicsDBImport - Complete VCF Header will be written to /mnt/output.gatk/genomicsdb.pseudochr1/vcfheader.vcf 18:30:14.201 INFO GenomicsDBImport - Importing to array - /mnt/output.gatk/genomicsdb.pseudochr1/genomicsdb_array 18:30:14.201 INFO ProgressMeter - Starting traversal 18:30:14.203 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 18:30:14.651 INFO GenomicsDBImport - Importing batch 1 with 5 samples 18:30:18.218 INFO GenomicsDBImport - Done importing batch 1/3 18:30:18.410 INFO GenomicsDBImport - Importing batch 2 with 5 samples 18:30:21.398 INFO GenomicsDBImport - Done importing batch 2/3 18:30:21.489 INFO GenomicsDBImport - Importing batch 3 with 2 samples 18:30:24.009 INFO GenomicsDBImport - Done importing batch 3/3 18:30:24.016 INFO ProgressMeter - pseudochr1:1 0.2 3 18.4 18:30:24.018 INFO ProgressMeter - Traversal complete. Processed 3 total batches in 0.2 minutes. 18:30:24.019 INFO GenomicsDBImport - Import of all batches to GenomicsDB completed! 18:30:24.020 INFO GenomicsDBImport - Shutting down engine [September 17, 2019 6:30:24 PM GMT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.21 minutes. Runtime.totalMemory()=2307915776 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.pseudochr1 --batch-size 5 -L pseudochr1 --sample-name-map gvcf.list.txt3 --reader-threads 1 18:30:30.195 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 18:30:32.200 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:32.202 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.0.0 18:30:32.203 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 18:30:32.204 INFO GenotypeGVCFs - Executing as user2@m256 on Linux v3.10.0-514.el7.x86_64 amd64 18:30:32.205 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01 18:30:32.207 INFO GenotypeGVCFs - Start Date/Time: September 17, 2019 6:30:30 PM GMT 18:30:32.207 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:32.208 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:30:32.210 INFO GenotypeGVCFs - HTSJDK Version: 2.18.2 18:30:32.211 INFO GenotypeGVCFs - Picard Version: 2.18.25 18:30:32.212 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 18:30:32.213 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 18:30:32.214 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 18:30:32.215 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 18:30:32.216 INFO GenotypeGVCFs - Deflater: IntelDeflater 18:30:32.217 INFO GenotypeGVCFs - Inflater: IntelInflater 18:30:32.218 INFO GenotypeGVCFs - GCS max retries/reopens: 20 18:30:32.219 INFO GenotypeGVCFs - Requester pays: disabled 18:30:32.220 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 18:30:35.677 INFO IntervalArgumentCollection - Processing 10010372 bp from intervals 18:30:35.695 INFO GenotypeGVCFs - Done initializing engine 18:30:35.816 INFO ProgressMeter - Starting traversal 18:30:35.818 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 18:30:54.255 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.287 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.332 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.340 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.347 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.354 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.395 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.406 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.413 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.419 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.426 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.478 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.485 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.492 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.498 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.561 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.595 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.600 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.605 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.609 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.617 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.630 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.634 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.640 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.646 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.651 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.660 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.666 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.670 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.674 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.680 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.692 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.696 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.706 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.710 INFO ProgressMeter - pseudochr1:245194 0.3 1000 3176.3 18:30:54.715 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.770 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.793 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.800 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.805 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.810 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.817 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.823 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.830 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.839 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.845 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.871 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.880 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.889 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.896 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.914 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.921 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.930 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.933 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.941 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.953 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.957 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.963 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.971 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.974 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.979 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.994 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:54.998 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.002 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.005 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.007 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.010 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.014 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.016 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.024 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.027 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.034 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.037 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.041 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.047 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.051 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.058 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.064 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.068 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.071 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.074 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.081 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.087 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.091 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.096 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.101 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.104 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.107 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.111 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.115 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.117 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.122 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.126 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.130 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.134 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.137 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.146 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.149 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.152 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.155 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.158 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.162 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.165 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.167 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.171 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.184 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.190 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.197 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.200 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.203 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.223 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.227 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.231 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.233 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.236 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.239 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.247 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.253 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.256 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.259 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.263 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.266 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.269 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.272 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.279 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.286 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.291 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.294 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.301 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.303 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.307 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.313 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.316 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.320 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.324 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.326 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.328 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.333 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.335 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.338 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.341 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.344 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.346 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.349 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.352 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.355 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.358 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.362 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.364 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.366 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.369 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.373 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.376 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.379 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.381 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.384 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.387 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.389 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.393 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.396 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.399 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.411 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.424 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.427 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.429 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.434 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.436 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.444 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.449 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.453 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.456 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.458 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.461 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.463 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.465 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.468 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.470 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.473 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.475 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.477 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.483 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.488 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.495 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.550 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.561 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.564 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.571 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.580 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.582 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.590 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.593 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.603 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.606 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.614 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.630 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.632 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.635 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.702 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.709 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.712 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.724 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.726 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.728 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.731 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.734 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.740 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.743 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.747 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.752 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.770 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.773 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.775 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.777 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.781 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.783 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.785 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.790 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.792 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.795 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.798 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.801 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.806 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.808 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.812 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.815 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.817 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.819 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.821 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.823 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.826 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.829 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.832 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.836 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.840 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.843 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.845 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.847 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.854 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.857 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.860 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.863 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.875 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.880 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.903 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.907 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.930 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.933 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.938 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.941 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.944 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.954 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.956 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.958 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.965 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.967 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.970 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.973 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.975 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples 18:30:55.978 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.20572321500000051,Cpu time(s),0.1974271809999994 18:30:56.001 INFO ProgressMeter - pseudochr1:7179440 0.3 8207 24399.0 18:30:56.002 INFO ProgressMeter - Traversal complete. Processed 8207 total variants in 0.3 minutes. 18:30:56.032 INFO GenotypeGVCFs - Shutting down engine [September 17, 2019 6:30:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.43 minutes. Runtime.totalMemory()=2351431680 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.pseudochr1.vcf.gz -V gendb://output.gatk/genomicsdb.pseudochr1 -L pseudochr1