Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenomicsDBImport --genomicsdb-workspace-path GenomicsDB/ -L intervals.bed --sample-name-map sample_map.txt --reader-threads 40 09:58:02.285 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jun 02, 2022 9:58:02 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:58:02.381 INFO GenomicsDBImport - ------------------------------------------------------------ 09:58:02.381 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.5.0 09:58:02.381 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:58:02.381 INFO GenomicsDBImport - Executing as sr320@raven on Linux v5.4.0-113-generic amd64 09:58:02.381 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v11.0.15+10-Ubuntu-0ubuntu0.18.04.1 09:58:02.381 INFO GenomicsDBImport - Start Date/Time: June 2, 2022 at 9:58:02 AM PDT 09:58:02.381 INFO GenomicsDBImport - ------------------------------------------------------------ 09:58:02.382 INFO GenomicsDBImport - ------------------------------------------------------------ 09:58:02.382 INFO GenomicsDBImport - HTSJDK Version: 2.24.1 09:58:02.382 INFO GenomicsDBImport - Picard Version: 2.25.4 09:58:02.382 INFO GenomicsDBImport - Built for Spark Version: 2.4.5 09:58:02.382 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:58:02.382 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:58:02.382 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:58:02.382 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:58:02.382 INFO GenomicsDBImport - Deflater: IntelDeflater 09:58:02.383 INFO GenomicsDBImport - Inflater: IntelInflater 09:58:02.383 INFO GenomicsDBImport - GCS max retries/reopens: 20 09:58:02.383 INFO GenomicsDBImport - Requester pays: disabled 09:58:02.383 INFO GenomicsDBImport - Initializing engine 09:58:02.402 INFO GenomicsDBImport - Shutting down engine [June 2, 2022 at 9:58:02 AM PDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2155872256 *********************************************************************** A USER ERROR has occurred: Failed to create reader from file:///home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/S12M.variants.g.vcf because of the following error: An index is required, but none found., for input source: file:///home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/S12M.variants.g.vcf *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenomicsDBImport --genomicsdb-workspace-path GenomicsDB/ -L intervals.bed --sample-name-map sample_map.txt --reader-threads 40 10:03:57.457 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jun 02, 2022 10:03:57 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 10:03:57.552 INFO GenomicsDBImport - ------------------------------------------------------------ 10:03:57.552 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.5.0 10:03:57.552 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 10:03:57.552 INFO GenomicsDBImport - Executing as sr320@raven on Linux v5.4.0-113-generic amd64 10:03:57.552 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v11.0.15+10-Ubuntu-0ubuntu0.18.04.1 10:03:57.552 INFO GenomicsDBImport - Start Date/Time: June 2, 2022 at 10:03:57 AM PDT 10:03:57.552 INFO GenomicsDBImport - ------------------------------------------------------------ 10:03:57.552 INFO GenomicsDBImport - ------------------------------------------------------------ 10:03:57.553 INFO GenomicsDBImport - HTSJDK Version: 2.24.1 10:03:57.553 INFO GenomicsDBImport - Picard Version: 2.25.4 10:03:57.553 INFO GenomicsDBImport - Built for Spark Version: 2.4.5 10:03:57.553 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 10:03:57.553 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 10:03:57.553 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 10:03:57.553 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 10:03:57.553 INFO GenomicsDBImport - Deflater: IntelDeflater 10:03:57.553 INFO GenomicsDBImport - Inflater: IntelInflater 10:03:57.553 INFO GenomicsDBImport - GCS max retries/reopens: 20 10:03:57.553 INFO GenomicsDBImport - Requester pays: disabled 10:03:57.554 INFO GenomicsDBImport - Initializing engine 10:03:57.994 INFO FeatureManager - Using codec BEDCodec to read file file:///home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/intervals.bed 10:03:58.011 INFO IntervalArgumentCollection - Processing 684741128 bp from intervals 10:03:58.014 INFO GenomicsDBImport - Done initializing engine 10:03:58.372 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a 10:03:58.372 INFO GenomicsDBImport - Vid Map JSON file will be written to /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB/vidmap.json 10:03:58.372 INFO GenomicsDBImport - Callset Map JSON file will be written to /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB/callset.json 10:03:58.372 INFO GenomicsDBImport - Complete VCF Header will be written to /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB/vcfheader.vcf 10:03:58.373 INFO GenomicsDBImport - Importing to workspace - /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB 10:03:58.373 WARN GenomicsDBImport - GenomicsDBImport cannot use multiple VCF reader threads for initialization when the number of intervals is greater than 1. Falling back to serial VCF reader initialization. 10:04:02.569 INFO GenomicsDBImport - Importing batch 1 with 26 samples 10:22:20.158 INFO GenomicsDBImport - Importing batch 1 with 26 samples 10:41:32.033 INFO GenomicsDBImport - Importing batch 1 with 26 samples 11:03:05.979 INFO GenomicsDBImport - Importing batch 1 with 26 samples 11:21:21.138 INFO GenomicsDBImport - Importing batch 1 with 26 samples 11:51:52.640 INFO GenomicsDBImport - Importing batch 1 with 26 samples 12:01:22.014 INFO GenomicsDBImport - Importing batch 1 with 26 samples 12:12:14.964 INFO GenomicsDBImport - Importing batch 1 with 26 samples 12:27:21.158 INFO GenomicsDBImport - Importing batch 1 with 26 samples 12:46:11.446 INFO GenomicsDBImport - Importing batch 1 with 26 samples 12:53:11.047 INFO GenomicsDBImport - Importing batch 1 with 26 samples 12:53:13.412 INFO GenomicsDBImport - Done importing batch 1/1 12:53:13.414 INFO GenomicsDBImport - Import completed! 12:53:13.414 INFO GenomicsDBImport - Shutting down engine [June 2, 2022 at 12:53:13 PM PDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 169.27 minutes. Runtime.totalMemory()=8313110528 Tool returned: true Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenomicsDBImport --genomicsdb-workspace-path GenomicsDB/ -L intervals.bed --sample-name-map sample_map.txt --reader-threads 40 07:48:52.050 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jun 08, 2022 7:48:52 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 07:48:52.147 INFO GenomicsDBImport - ------------------------------------------------------------ 07:48:52.147 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.5.0 07:48:52.147 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 07:48:52.147 INFO GenomicsDBImport - Executing as sr320@raven on Linux v5.4.0-113-generic amd64 07:48:52.147 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v11.0.15+10-Ubuntu-0ubuntu0.18.04.1 07:48:52.147 INFO GenomicsDBImport - Start Date/Time: June 8, 2022 at 7:48:52 AM PDT 07:48:52.148 INFO GenomicsDBImport - ------------------------------------------------------------ 07:48:52.148 INFO GenomicsDBImport - ------------------------------------------------------------ 07:48:52.148 INFO GenomicsDBImport - HTSJDK Version: 2.24.1 07:48:52.148 INFO GenomicsDBImport - Picard Version: 2.25.4 07:48:52.148 INFO GenomicsDBImport - Built for Spark Version: 2.4.5 07:48:52.148 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 07:48:52.148 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 07:48:52.148 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 07:48:52.148 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 07:48:52.148 INFO GenomicsDBImport - Deflater: IntelDeflater 07:48:52.148 INFO GenomicsDBImport - Inflater: IntelInflater 07:48:52.149 INFO GenomicsDBImport - GCS max retries/reopens: 20 07:48:52.149 INFO GenomicsDBImport - Requester pays: disabled 07:48:52.149 INFO GenomicsDBImport - Initializing engine 07:48:52.150 INFO GenomicsDBImport - Shutting down engine [June 8, 2022 at 7:48:52 AM PDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2155872256 *********************************************************************** A USER ERROR has occurred: Bad input: Found two mappings for the same sample: S12M S12M.variants.g.vcf S12M.variants.g.vcf *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenomicsDBImport --genomicsdb-workspace-path GenomicsDB/ -L intervals.bed --sample-name-map sample_map.txt --reader-threads 40 07:56:02.121 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jun 08, 2022 7:56:02 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 07:56:02.222 INFO GenomicsDBImport - ------------------------------------------------------------ 07:56:02.223 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.5.0 07:56:02.223 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 07:56:02.223 INFO GenomicsDBImport - Executing as sr320@raven on Linux v5.4.0-113-generic amd64 07:56:02.223 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v11.0.15+10-Ubuntu-0ubuntu0.18.04.1 07:56:02.223 INFO GenomicsDBImport - Start Date/Time: June 8, 2022 at 7:56:02 AM PDT 07:56:02.223 INFO GenomicsDBImport - ------------------------------------------------------------ 07:56:02.223 INFO GenomicsDBImport - ------------------------------------------------------------ 07:56:02.224 INFO GenomicsDBImport - HTSJDK Version: 2.24.1 07:56:02.224 INFO GenomicsDBImport - Picard Version: 2.25.4 07:56:02.224 INFO GenomicsDBImport - Built for Spark Version: 2.4.5 07:56:02.224 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 07:56:02.224 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 07:56:02.224 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 07:56:02.224 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 07:56:02.224 INFO GenomicsDBImport - Deflater: IntelDeflater 07:56:02.224 INFO GenomicsDBImport - Inflater: IntelInflater 07:56:02.224 INFO GenomicsDBImport - GCS max retries/reopens: 20 07:56:02.224 INFO GenomicsDBImport - Requester pays: disabled 07:56:02.224 INFO GenomicsDBImport - Initializing engine 07:56:02.225 INFO GenomicsDBImport - Shutting down engine [June 8, 2022 at 7:56:02 AM PDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2155872256 *********************************************************************** A USER ERROR has occurred: Bad input: Found two mappings for the same sample: S12M S12M.variants.g.vcf S12M.variants.g.vcf *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenomicsDBImport --genomicsdb-workspace-path GenomicsDB/ -L intervals.bed --sample-name-map sample_map.txt --reader-threads 40 07:39:10.641 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jun 11, 2022 7:39:10 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 07:39:10.737 INFO GenomicsDBImport - ------------------------------------------------------------ 07:39:10.737 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.5.0 07:39:10.738 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 07:39:10.738 INFO GenomicsDBImport - Executing as sr320@raven on Linux v5.4.0-113-generic amd64 07:39:10.738 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v11.0.15+10-Ubuntu-0ubuntu0.18.04.1 07:39:10.738 INFO GenomicsDBImport - Start Date/Time: June 11, 2022 at 7:39:10 AM PDT 07:39:10.738 INFO GenomicsDBImport - ------------------------------------------------------------ 07:39:10.738 INFO GenomicsDBImport - ------------------------------------------------------------ 07:39:10.738 INFO GenomicsDBImport - HTSJDK Version: 2.24.1 07:39:10.739 INFO GenomicsDBImport - Picard Version: 2.25.4 07:39:10.739 INFO GenomicsDBImport - Built for Spark Version: 2.4.5 07:39:10.739 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 07:39:10.739 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 07:39:10.739 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 07:39:10.739 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 07:39:10.739 INFO GenomicsDBImport - Deflater: IntelDeflater 07:39:10.739 INFO GenomicsDBImport - Inflater: IntelInflater 07:39:10.739 INFO GenomicsDBImport - GCS max retries/reopens: 20 07:39:10.739 INFO GenomicsDBImport - Requester pays: disabled 07:39:10.739 INFO GenomicsDBImport - Initializing engine 07:39:11.090 INFO FeatureManager - Using codec BEDCodec to read file file:///home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/intervals.bed 07:39:11.094 INFO IntervalArgumentCollection - Processing 684741128 bp from intervals 07:39:11.096 INFO GenomicsDBImport - Done initializing engine 07:39:11.375 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a 07:39:11.376 INFO GenomicsDBImport - Vid Map JSON file will be written to /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB/vidmap.json 07:39:11.376 INFO GenomicsDBImport - Callset Map JSON file will be written to /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB/callset.json 07:39:11.376 INFO GenomicsDBImport - Complete VCF Header will be written to /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB/vcfheader.vcf 07:39:11.376 INFO GenomicsDBImport - Importing to workspace - /home/shared/8TB_HDD_01/sr320/github/ceabigr/output/11-RNAseq-snps/GenomicsDB 07:39:11.376 WARN GenomicsDBImport - GenomicsDBImport cannot use multiple VCF reader threads for initialization when the number of intervals is greater than 1. Falling back to serial VCF reader initialization. 07:39:14.474 INFO GenomicsDBImport - Importing batch 1 with 26 samples 07:56:21.624 INFO GenomicsDBImport - Importing batch 1 with 26 samples 08:14:23.142 INFO GenomicsDBImport - Importing batch 1 with 26 samples 08:34:51.982 INFO GenomicsDBImport - Importing batch 1 with 26 samples 08:52:02.755 INFO GenomicsDBImport - Importing batch 1 with 26 samples 09:20:59.104 INFO GenomicsDBImport - Importing batch 1 with 26 samples 09:29:53.075 INFO GenomicsDBImport - Importing batch 1 with 26 samples 09:40:06.517 INFO GenomicsDBImport - Importing batch 1 with 26 samples 09:54:14.089 INFO GenomicsDBImport - Importing batch 1 with 26 samples 10:11:57.494 INFO GenomicsDBImport - Importing batch 1 with 26 samples 10:18:31.734 INFO GenomicsDBImport - Importing batch 1 with 26 samples 10:18:34.076 INFO GenomicsDBImport - Done importing batch 1/1 10:18:34.077 INFO GenomicsDBImport - Import completed! 10:18:34.078 INFO GenomicsDBImport - Shutting down engine [June 11, 2022 at 10:18:34 AM PDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 159.39 minutes. Runtime.totalMemory()=9407823872 Tool returned: true