19:01:55.298 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
19:01:55.388 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
19:01:55.711 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:01:55.716 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:01:55.718 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:01:55.721 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:01:55.722 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:01:55.726 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:01:55.761 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
19:01:55.792 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:01:55.808 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
19:01:55.812 INFO ProgressMeter - Starting traversal
19:01:55.812 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:55.812 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:55.813 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:55.933 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:01:55.933 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:55.933 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:55.934 INFO TestGATKToolWithFeatures - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:55.934 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:55.934 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 7:01:55 PM GMT
19:01:55.934 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:01:55.934 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:01:55.934 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:55.934 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:55.934 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:55.934 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:55.934 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
19:01:55.934 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
19:01:55.934 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
19:01:55.934 INFO TestGATKToolWithFeatures - Requester pays: disabled
19:01:55.934 INFO TestGATKToolWithFeatures - Initializing engine
19:01:55.936 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
19:01:55.937 INFO TestGATKToolWithFeatures - Done initializing engine
19:01:55.937 INFO ProgressMeter - Starting traversal
19:01:55.937 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:55.937 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:55.937 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:55.937 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 7:01:55 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:55.990 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:55.990 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:55.990 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:55.990 INFO TestIntervalTransformingWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:55.990 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:55.990 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 7:01:55 PM GMT
19:01:55.990 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:55.990 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:55.990 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:55.990 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:55.990 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:55.991 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:55.991 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:01:55.991 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:01:55.991 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:01:55.991 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:01:55.991 INFO TestIntervalTransformingWalker - Initializing engine
19:01:55.992 INFO IntervalArgumentCollection - Processing 1 bp from intervals
19:01:55.993 INFO TestIntervalTransformingWalker - Done initializing engine
19:01:55.993 INFO ProgressMeter - Starting traversal
19:01:55.993 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:55.993 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:55.993 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:55.993 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 7:01:55 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:56.008 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.008 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.009 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.009 INFO TestIntervalTransformingWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.009 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.009 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.009 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.009 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.009 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.009 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.009 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.009 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.009 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:01:56.009 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:01:56.009 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:01:56.009 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:01:56.009 INFO TestIntervalTransformingWalker - Initializing engine
19:01:56.010 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
19:01:56.010 INFO TestIntervalTransformingWalker - Done initializing engine
19:01:56.011 INFO ProgressMeter - Starting traversal
19:01:56.011 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.011 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.011 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.011 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:56.027 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.027 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.027 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.027 INFO TestIntervalTransformingWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.027 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.027 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.027 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.027 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.027 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.027 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.027 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.028 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.028 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:01:56.028 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:01:56.028 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:01:56.028 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:01:56.028 INFO TestIntervalTransformingWalker - Initializing engine
19:01:56.029 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
19:01:56.029 INFO TestIntervalTransformingWalker - Done initializing engine
19:01:56.029 INFO ProgressMeter - Starting traversal
19:01:56.029 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.029 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.029 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.029 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:56.045 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.045 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.045 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.045 INFO TestIntervalTransformingWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.045 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.045 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.045 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.045 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.045 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.045 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.045 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.046 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.046 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:01:56.046 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:01:56.046 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:01:56.046 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:01:56.046 INFO TestIntervalTransformingWalker - Initializing engine
19:01:56.047 INFO TestIntervalTransformingWalker - Done initializing engine
19:01:56.047 INFO ProgressMeter - Starting traversal
19:01:56.047 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.047 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.047 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.047 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:56.066 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.067 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.067 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.067 INFO TestIntervalTransformingWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.067 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.067 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.067 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.067 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:01:56.067 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.067 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.067 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.067 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.067 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:01:56.067 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:01:56.067 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:01:56.067 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:01:56.067 INFO TestIntervalTransformingWalker - Initializing engine
19:01:56.067 INFO TestIntervalTransformingWalker - Done initializing engine
19:01:56.067 INFO ProgressMeter - Starting traversal
19:01:56.068 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.068 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.068 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.068 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:56.084 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.084 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.084 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.084 INFO TestIntervalWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.084 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.084 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.084 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.084 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.084 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.084 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.084 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.084 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.084 INFO TestIntervalWalker - Deflater: IntelDeflater
19:01:56.084 INFO TestIntervalWalker - Inflater: IntelInflater
19:01:56.085 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:01:56.085 INFO TestIntervalWalker - Requester pays: disabled
19:01:56.085 INFO TestIntervalWalker - Initializing engine
19:01:56.086 INFO IntervalArgumentCollection - Processing 1 bp from intervals
19:01:56.086 INFO TestIntervalWalker - Done initializing engine
19:01:56.086 INFO ProgressMeter - Starting traversal
19:01:56.086 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.086 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.086 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.086 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:56.102 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.102 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.102 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.103 INFO TestIntervalWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.103 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.103 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.103 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.103 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.103 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.103 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.103 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.103 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.103 INFO TestIntervalWalker - Deflater: IntelDeflater
19:01:56.103 INFO TestIntervalWalker - Inflater: IntelInflater
19:01:56.103 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:01:56.103 INFO TestIntervalWalker - Requester pays: disabled
19:01:56.103 INFO TestIntervalWalker - Initializing engine
19:01:56.104 INFO TestIntervalWalker - Done initializing engine
19:01:56.104 INFO ProgressMeter - Starting traversal
19:01:56.104 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.104 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.104 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.104 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:56.121 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.121 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.121 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.121 INFO TestIntervalWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.121 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.121 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.121 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.121 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.121 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.121 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.121 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.121 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.121 INFO TestIntervalWalker - Deflater: IntelDeflater
19:01:56.121 INFO TestIntervalWalker - Inflater: IntelInflater
19:01:56.121 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:01:56.121 INFO TestIntervalWalker - Requester pays: disabled
19:01:56.121 INFO TestIntervalWalker - Initializing engine
19:01:56.121 INFO TestIntervalWalker - Done initializing engine
19:01:56.121 INFO ProgressMeter - Starting traversal
19:01:56.121 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.122 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.122 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.122 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:4.6.2.0-5-g0192957-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
19:01:56.318 INFO FeatureManager - Using codec IntervalListCodec to read file file:///gatkCloneMountPoint/src/test/resources/picard_intervals.interval_list
19:01:56.321 INFO IntervalArgumentCollection - Processing 20 bp from intervals
19:01:56.321 INFO ProgressMeter - Starting traversal
19:01:56.321 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.321 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.321 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.336 INFO ProgressMeter - Starting traversal
19:01:56.336 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.336 INFO ProgressMeter - unmapped 0.0 0 NaN
19:01:56.336 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.356 INFO ProgressMeter - Starting traversal
19:01:56.356 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
19:01:56.416 INFO ProgressMeter - unmapped 0.0 0 0.0
19:01:56.416 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.433 INFO ProgressMeter - Starting traversal
19:01:56.433 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.455 INFO ProgressMeter - unmapped 0.0 0 0.0
19:01:56.455 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:56.474 INFO ProgressMeter - Starting traversal
19:01:56.474 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:01:56.505 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.506 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.506 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.506 INFO TestIntervalWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.506 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.506 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.506 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.506 INFO TestIntervalWalker - ------------------------------------------------------------
19:01:56.506 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.506 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.506 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.506 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.506 INFO TestIntervalWalker - Deflater: IntelDeflater
19:01:56.506 INFO TestIntervalWalker - Inflater: IntelInflater
19:01:56.506 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:01:56.506 INFO TestIntervalWalker - Requester pays: disabled
19:01:56.506 INFO TestIntervalWalker - Initializing engine
19:01:56.506 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864