21:17:50.488 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
21:17:50.549 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
21:17:50.878 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
21:17:50.882 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
21:17:50.883 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
21:17:50.887 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
21:17:50.889 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
21:17:50.893 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
21:17:50.927 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
21:17:50.956 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
21:17:50.973 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
21:17:50.977 INFO ProgressMeter - Starting traversal
21:17:50.977 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:50.977 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:50.977 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.101 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
21:17:51.101 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.101 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.102 INFO TestGATKToolWithFeatures - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.102 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.102 INFO TestGATKToolWithFeatures - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.102 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
21:17:51.102 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
21:17:51.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.103 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
21:17:51.103 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
21:17:51.103 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
21:17:51.103 INFO TestGATKToolWithFeatures - Requester pays: disabled
21:17:51.103 INFO TestGATKToolWithFeatures - Initializing engine
21:17:51.104 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
21:17:51.106 INFO TestGATKToolWithFeatures - Done initializing engine
21:17:51.106 INFO ProgressMeter - Starting traversal
21:17:51.106 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.106 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.106 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.106 INFO TestGATKToolWithFeatures - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.155 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.155 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.155 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.155 INFO TestIntervalTransformingWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.155 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.155 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.155 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.155 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.155 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.155 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.156 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.156 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.156 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
21:17:51.156 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
21:17:51.156 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
21:17:51.156 INFO TestIntervalTransformingWalker - Requester pays: disabled
21:17:51.156 INFO TestIntervalTransformingWalker - Initializing engine
21:17:51.157 INFO IntervalArgumentCollection - Processing 1 bp from intervals
21:17:51.158 INFO TestIntervalTransformingWalker - Done initializing engine
21:17:51.158 INFO ProgressMeter - Starting traversal
21:17:51.158 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.158 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.158 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.158 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.175 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.175 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.175 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.175 INFO TestIntervalTransformingWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.175 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.175 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.175 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.175 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.176 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.176 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.176 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.176 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.176 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
21:17:51.176 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
21:17:51.176 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
21:17:51.176 INFO TestIntervalTransformingWalker - Requester pays: disabled
21:17:51.176 INFO TestIntervalTransformingWalker - Initializing engine
21:17:51.177 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
21:17:51.177 INFO TestIntervalTransformingWalker - Done initializing engine
21:17:51.177 INFO ProgressMeter - Starting traversal
21:17:51.177 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.177 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.177 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.177 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.195 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.195 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.195 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.195 INFO TestIntervalTransformingWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.195 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.195 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.195 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.195 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.195 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.195 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.195 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.195 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.195 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
21:17:51.196 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
21:17:51.196 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
21:17:51.196 INFO TestIntervalTransformingWalker - Requester pays: disabled
21:17:51.196 INFO TestIntervalTransformingWalker - Initializing engine
21:17:51.197 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
21:17:51.197 INFO TestIntervalTransformingWalker - Done initializing engine
21:17:51.197 INFO ProgressMeter - Starting traversal
21:17:51.197 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.197 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.197 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.197 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.214 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.214 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.214 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.214 INFO TestIntervalTransformingWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.214 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.214 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.214 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.214 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.214 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.214 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.214 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.214 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.214 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
21:17:51.214 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
21:17:51.214 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
21:17:51.214 INFO TestIntervalTransformingWalker - Requester pays: disabled
21:17:51.215 INFO TestIntervalTransformingWalker - Initializing engine
21:17:51.215 INFO TestIntervalTransformingWalker - Done initializing engine
21:17:51.215 INFO ProgressMeter - Starting traversal
21:17:51.215 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.215 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.216 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.216 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.233 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.233 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.233 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.233 INFO TestIntervalTransformingWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.233 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.233 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.233 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.233 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
21:17:51.233 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.233 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.233 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.233 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.233 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
21:17:51.234 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
21:17:51.234 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
21:17:51.234 INFO TestIntervalTransformingWalker - Requester pays: disabled
21:17:51.234 INFO TestIntervalTransformingWalker - Initializing engine
21:17:51.234 INFO TestIntervalTransformingWalker - Done initializing engine
21:17:51.234 INFO ProgressMeter - Starting traversal
21:17:51.234 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.234 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.234 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.234 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.252 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.253 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.253 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.253 INFO TestIntervalWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.253 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.253 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.253 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.253 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.253 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.253 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.253 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.253 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.253 INFO TestIntervalWalker - Deflater: IntelDeflater
21:17:51.253 INFO TestIntervalWalker - Inflater: IntelInflater
21:17:51.253 INFO TestIntervalWalker - GCS max retries/reopens: 20
21:17:51.253 INFO TestIntervalWalker - Requester pays: disabled
21:17:51.254 INFO TestIntervalWalker - Initializing engine
21:17:51.254 INFO IntervalArgumentCollection - Processing 1 bp from intervals
21:17:51.254 INFO TestIntervalWalker - Done initializing engine
21:17:51.254 INFO ProgressMeter - Starting traversal
21:17:51.255 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.255 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.255 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.255 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.271 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.271 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.271 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.271 INFO TestIntervalWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.271 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.271 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.271 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.271 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.271 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.272 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.272 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.272 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.272 INFO TestIntervalWalker - Deflater: IntelDeflater
21:17:51.272 INFO TestIntervalWalker - Inflater: IntelInflater
21:17:51.272 INFO TestIntervalWalker - GCS max retries/reopens: 20
21:17:51.272 INFO TestIntervalWalker - Requester pays: disabled
21:17:51.272 INFO TestIntervalWalker - Initializing engine
21:17:51.273 INFO TestIntervalWalker - Done initializing engine
21:17:51.273 INFO ProgressMeter - Starting traversal
21:17:51.273 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.273 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.273 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.273 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:51.288 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.289 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.289 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.289 INFO TestIntervalWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.289 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.289 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.289 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.289 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.289 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.289 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.289 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.289 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.289 INFO TestIntervalWalker - Deflater: IntelDeflater
21:17:51.289 INFO TestIntervalWalker - Inflater: IntelInflater
21:17:51.289 INFO TestIntervalWalker - GCS max retries/reopens: 20
21:17:51.289 INFO TestIntervalWalker - Requester pays: disabled
21:17:51.289 INFO TestIntervalWalker - Initializing engine
21:17:51.290 INFO TestIntervalWalker - Done initializing engine
21:17:51.290 INFO ProgressMeter - Starting traversal
21:17:51.290 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.290 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.290 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.290 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:4.6.1.0-11-g40db79c-SNAPSHOT
Optional Arguments:
--add-output-sam-program-record <Boolean>
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}
--add-output-vcf-command-line <Boolean>
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}
--annotation,-A <String> One or more specific annotations to add to variant calls This argument may be specified 0
or more times. Default value: null. Possible values: {AlleleFraction, AllelePseudoDepth,
AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
AS_StrandBiasMutectAnnotation, AS_StrandOddsRatio, AssemblyComplexity, BaseQuality,
BaseQualityHistogram, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest,
CountNs, Coverage, CycleSkipStatus, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet,
FisherStrand, FragmentDepthPerAlleleBySample, FragmentLength, GcContent,
GenotypeSummaries, HaplotypeFilteringAnnotation, HmerIndelLength, HmerIndelNuc,
HmerMotifs, InbreedingCoeff, IndelClassify, IndelLength, LikelihoodRankSumTest,
MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts,
OriginalAlignment, PossibleDeNovo, QualByDepth, RawGtCount, ReadPosition,
ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample,
StrandOddsRatio, TandemRepeat, TransmittedSingleton, UniqueAltReadCount, VariantType}
--annotation-group,-G <String>One or more groups of annotations to apply to variant calls This argument may be
specified 0 or more times. Default value: null. Possible values:
{AlleleSpecificAnnotation, AS_StandardAnnotation, GenotypeAnnotation, InfoFieldAnnotation,
JumboGenotypeAnnotation, JumboInfoAnnotation, ReducibleAnnotation, StandardAnnotation,
StandardFlowBasedAnnotation, StandardHCAnnotation, StandardMutectAnnotation,
VariantAnnotation}
--annotations-to-exclude,-AX <String>
One or more specific annotations to exclude from variant calls This argument may be
specified 0 or more times. Default value: null. Any value allowed
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--cloud-index-prefetch-buffer,-CIPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
cloudPrefetchBuffer if unset. Default value: -1.
--cloud-prefetch-buffer,-CPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
--create-output-bam-index,-OBI <Boolean>
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}
--create-output-bam-md5,-OBM <Boolean>
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}
--create-output-variant-index,-OVI <Boolean>
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}
--create-output-variant-md5,-OVM <Boolean>
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}
--disable-bam-index-caching,-DBIC <Boolean>
If true, don't cache bam indexes, this will reduce memory requirements but may harm
performance if many intervals are specified. Caching is automatically disabled if there
are no intervals specified. Default value: false. Possible values: {true, false}
--disable-read-filter,-DF <String>
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {WellformedReadFilter}
--disable-sequence-dictionary-validation <Boolean>
If specified, do not check the sequence dictionaries from our inputs for compatibility.
Use at your own risk! Default value: false. Possible values: {true, false}
--exclude-intervals,-XL <String>
One or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.
--flow-order-for-annotations <String>
flow order used for this annotations. [readGroup:]flowOrder This argument may be
specified 0 or more times. Default value: null.
--founder-id <String> Samples representing the population "founders" This argument may be specified 0 or more
times. Default value: null.
--gatk-config-file <String> A configuration file to use with the GATK. Default value: null.
--gcs-max-retries,-gcs-retries <Integer>
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.
--gcs-project-for-requester-pays <String>
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. User must have storage.buckets.get permission on the bucket being accessed.
Default value: .
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--input,-I <GATKPath> BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
Default value: null.
--interval-exclusion-padding,-ixp <Integer>
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
--interval-merging-rule,-imr <IntervalMergingRule>
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}
--interval-padding,-ip <Integer>
Amount of padding (in bp) to add to each interval you are including. Default value: 0.
--interval-set-rule,-isr <IntervalSetRule>
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}
--intervals,-L <String> One or more genomic intervals over which to operate This argument may be specified 0 or
more times. Default value: null.
--inverted-read-filter,-XRF <String>
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis
(after regular read filters). This argument may be specified 0 or more times. Default
value: null.
--lenient,-LE <Boolean> Lenient processing of VCF files Default value: false. Possible values: {true, false}
--max-variants-per-shard <Integer>
If non-zero, partitions VCF output into shards, each containing up to the given number of
records. Default value: 0.
--output,-out <File> Input variants Default value: null.
--pedigree,-ped <GATKPath> Pedigree file for determining the population "founders" Default value: null.
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--read-filter,-RF <String> Read filters to be applied before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {AlignmentAgreesWithHeaderReadFilter,
AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
ExcessiveEndClippedReadFilter, FirstOfPairReadFilter,
FlowBasedTPAttributeSymetricReadFilter, FlowBasedTPAttributeValidReadFilter,
FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter,
HmerQualitySymetricReadFilter, IntervalOverlapReadFilter,
JexlExpressionReadTagValueFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupHasFlowOrderReadFilter,
ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter,
ReadNameReadFilter, ReadStrandFilter, ReadTagValueFilter, SampleReadFilter,
SecondOfPairReadFilter, SeqIsStoredReadFilter, SoftClippedReadFilter,
ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedFlowBasedReadFilter,
WellformedReadFilter}
--read-index <GATKPath> Indices to use for the read inputs. If specified, an index must be provided for every read
input and in the same order as the read inputs. If this argument is not specified, the
path to the index for each input will be inferred automatically. This argument may be
specified 0 or more times. Default value: null.
--read-validation-stringency,-VS <ValidationStringency>
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default
stringency value SILENT can improve performance when processing a BAM file in which
variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default
value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
--reference,-R <GATKPath> Reference sequence Default value: null.
--seconds-between-progress-updates <Double>
Output traversal statistics every time this many seconds elapse Default value: 10.0.
--sequence-dictionary <GATKPath>
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.
--sites-only-vcf-output <Boolean>
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}
--tmp-dir <GATKPath> Temp directory to use. Default value: null.
--use-jdk-deflater,-jdk-deflater <Boolean>
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}
--use-jdk-inflater,-jdk-inflater <Boolean>
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}
--verbosity <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--disable-tool-default-annotations <Boolean>
Disable all tool default annotations Default value: false. Possible values: {true, false}
--disable-tool-default-read-filters <Boolean>
Disable all tool default read filters (WARNING: many tools will not function correctly
without their default read filters on) Default value: false. Possible values: {true,
false}
--enable-all-annotations <Boolean>
Use all possible annotations (not for the faint of heart) Default value: false. Possible
values: {true, false}
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
Conditional Arguments for annotation:
Valid only if "AllelePseudoDepth" is specified:
--dirichlet-keep-prior-in-count <Boolean>
By default we don't keep the prior use in the output counts ase it makes it easier to
interpretthis quantity as the number of supporting reads specially in low depth sites. We
this toggled the prior is included Default value: false. Possible values: {true, false}
--dirichlet-prior-pseudo-count <Double>
Pseudo-count used as prior for all alleles. The default is 1.0 resulting in a flat prior
Default value: 1.0.
--pseudo-count-weight-decay-rate <Double>
A what rate the weight of a read decreases base on its informativeness; e.g. 1.0 is linear
decay (default), 2.0 is for quadratic decay Default value: 1.0.
Valid only if "AssemblyComplexity" is specified:
--assembly-complexity-reference-mode <Boolean>
If enabled will treat the reference as the basis for assembly complexity as opposed to
estimated germline haplotypes Default value: false. Possible values: {true, false}
Valid only if "PossibleDeNovo" is specified:
--denovo-depth-threshold <Integer>
Minimum depth (DP) for all trio members to be considered for de novo calculation. Default
value: 0.
--denovo-parent-gq-threshold <Integer>
Minimum genotype quality for parents to be considered for de novo calculation (separate
from GQ thershold for full trio). Default value: 20.
Valid only if "RMSMappingQuality" is specified:
--allow-old-rms-mapping-quality-annotation-data <Boolean>
Override to allow old RMSMappingQuality annotated VCFs to function Default value: false.
Possible values: {true, false}
Conditional Arguments for readFilter:
Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases <Integer>Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
overrides threshold fraction. Default value: null. Cannot be used in conjunction with
argument(s) maxAmbiguousBaseFraction
--ambig-filter-frac <Double> Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjunction
with argument(s) maxAmbiguousBases
Valid only if "ExcessiveEndClippedReadFilter" is specified:
--max-clipped-bases <Integer> Maximum number of clipped bases on either end of a given read Default value: 1000.
Valid only if "FlowBasedTPAttributeValidReadFilter" is specified:
--read-filter-max-hmer <Integer>
maxHmer to use for testing in the filter Default value: 12.
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length <Integer>
Maximum length of fragment (insert size) Default value: 1000000.
--min-fragment-length <Integer>
Minimum length of fragment (insert size) Default value: 0.
Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals <String> One or more genomic intervals to keep This argument must be specified at least once.
Required.
Valid only if "JexlExpressionReadTagValueFilter" is specified:
--read-filter-expression <String>
One or more JEXL expressions used to filter This argument must be specified at least
once. Required.
Valid only if "LibraryReadFilter" is specified:
--library <String> Name of the library to keep This argument must be specified at least once. Required.
Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality <Integer>
Maximum mapping quality to keep (inclusive) Default value: null.
--minimum-mapping-quality <Integer>
Minimum mapping quality to keep (inclusive) Default value: 10.
Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length <Integer>
Minimum start location difference at which mapped mates are considered distant Default
value: 1000.
Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends <Boolean>
Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
block Default value: false. Possible values: {true, false}
--filter-too-short <Integer> Minimum number of aligned bases Default value: 30.
Valid only if "PlatformReadFilter" is specified:
--platform-filter-name <String>
Platform attribute (PL) to match This argument must be specified at least once. Required.
Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes <String> Platform unit (PU) to filter out This argument must be specified at least once. Required.
Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list <String>
A read group filter expression in the form "attribute:value", where "attribute" is a two
character read group attribute such as "RG" or "PU". This argument must be specified at
least once. Required.
Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group <String> The name of the read group to keep Required.
Valid only if "ReadLengthReadFilter" is specified:
--max-read-length <Integer> Keep only reads with length at most equal to the specified value Required.
--min-read-length <Integer> Keep only reads with length at least equal to the specified value Default value: 1.
Valid only if "ReadNameReadFilter" is specified:
--read-name <String> Keep only reads with this read name This argument must be specified at least once.
Required.
Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only <Boolean>
Keep only reads on the reverse strand Required. Possible values: {true, false}
Valid only if "ReadTagValueFilter" is specified:
--read-filter-tag <String> Look for this tag in read Required.
--read-filter-tag-comp <Float>Compare value in tag to this value Default value: 0.0.
--read-filter-tag-op <Operator>
Compare value in tag to value with this operator. If T is the value in the tag, OP is the
operation provided, and V is the value in read-filter-tag, then the read will pass the
filter iff T OP V is true. Default value: EQUAL. Possible values: {LESS, LESS_OR_EQUAL,
GREATER, GREATER_OR_EQUAL, EQUAL, NOT_EQUAL}
Valid only if "SampleReadFilter" is specified:
--sample <String> The name of the sample(s) to keep, filtering out all others This argument must be
specified at least once. Required.
Valid only if "SoftClippedReadFilter" is specified:
--max-soft-clipped-leading-trailing-ratio <Double>
Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
in read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumSoftClippedRatio
--max-soft-clipped-ratio <Double>
Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumLeadingTrailingSoftClippedRatio
21:17:51.507 INFO FeatureManager - Using codec IntervalListCodec to read file file:///gatkCloneMountPoint/src/test/resources/picard_intervals.interval_list
21:17:51.509 INFO IntervalArgumentCollection - Processing 20 bp from intervals
21:17:51.510 INFO ProgressMeter - Starting traversal
21:17:51.510 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.510 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.510 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.525 INFO ProgressMeter - Starting traversal
21:17:51.525 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.525 INFO ProgressMeter - unmapped 0.0 0 NaN
21:17:51.525 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.545 INFO ProgressMeter - Starting traversal
21:17:51.546 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
21:17:51.604 INFO ProgressMeter - unmapped 0.0 0 0.0
21:17:51.604 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.624 INFO ProgressMeter - Starting traversal
21:17:51.624 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.646 INFO ProgressMeter - unmapped 0.0 0 0.0
21:17:51.646 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:51.663 INFO ProgressMeter - Starting traversal
21:17:51.664 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
21:17:51.693 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.694 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:51.694 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:51.694 INFO TestIntervalWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:51.694 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:51.694 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 9:17:51 PM GMT
21:17:51.694 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.694 INFO TestIntervalWalker - ------------------------------------------------------------
21:17:51.694 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:51.694 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:51.694 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:51.694 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:51.694 INFO TestIntervalWalker - Deflater: IntelDeflater
21:17:51.694 INFO TestIntervalWalker - Inflater: IntelInflater
21:17:51.694 INFO TestIntervalWalker - GCS max retries/reopens: 20
21:17:51.694 INFO TestIntervalWalker - Requester pays: disabled
21:17:51.694 INFO TestIntervalWalker - Initializing engine
21:17:51.694 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 9:17:51 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560