15:09:16.229 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
15:09:16.290 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
15:09:16.606 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
15:09:16.610 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
15:09:16.612 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
15:09:16.616 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
15:09:16.618 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
15:09:16.622 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
15:09:16.659 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
15:09:16.690 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
15:09:16.707 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
15:09:16.712 INFO ProgressMeter - Starting traversal
15:09:16.712 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.712 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.712 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.832 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:09:16.832 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:16.832 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:16.832 INFO TestGATKToolWithFeatures - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:16.832 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:16.832 INFO TestGATKToolWithFeatures - Start Date/Time: March 4, 2026 at 3:09:16 PM GMT
15:09:16.832 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:09:16.833 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:09:16.833 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:16.833 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:16.833 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:16.833 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:16.833 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
15:09:16.833 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
15:09:16.833 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
15:09:16.833 INFO TestGATKToolWithFeatures - Requester pays: disabled
15:09:16.833 INFO TestGATKToolWithFeatures - Initializing engine
15:09:16.835 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
15:09:16.836 INFO TestGATKToolWithFeatures - Done initializing engine
15:09:16.836 INFO ProgressMeter - Starting traversal
15:09:16.836 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.837 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.837 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.837 INFO TestGATKToolWithFeatures - Shutting down engine
[March 4, 2026 at 3:09:16 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:16.887 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.887 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:16.887 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:16.887 INFO TestIntervalTransformingWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:16.887 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:16.887 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 3:09:16 PM GMT
15:09:16.887 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.887 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.888 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:16.888 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:16.888 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:16.888 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:16.888 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
15:09:16.888 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
15:09:16.888 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
15:09:16.888 INFO TestIntervalTransformingWalker - Requester pays: disabled
15:09:16.888 INFO TestIntervalTransformingWalker - Initializing engine
15:09:16.889 INFO IntervalArgumentCollection - Processing 1 bp from intervals
15:09:16.890 INFO TestIntervalTransformingWalker - Done initializing engine
15:09:16.891 INFO ProgressMeter - Starting traversal
15:09:16.891 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.891 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.891 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.891 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 3:09:16 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:16.907 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.907 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:16.907 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:16.907 INFO TestIntervalTransformingWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:16.907 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:16.907 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 3:09:16 PM GMT
15:09:16.907 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.907 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.907 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:16.908 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:16.908 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:16.908 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:16.908 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
15:09:16.908 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
15:09:16.908 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
15:09:16.908 INFO TestIntervalTransformingWalker - Requester pays: disabled
15:09:16.908 INFO TestIntervalTransformingWalker - Initializing engine
15:09:16.909 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
15:09:16.909 INFO TestIntervalTransformingWalker - Done initializing engine
15:09:16.909 INFO ProgressMeter - Starting traversal
15:09:16.909 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.909 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.910 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.910 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 3:09:16 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:16.926 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.926 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:16.926 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:16.926 INFO TestIntervalTransformingWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:16.926 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:16.926 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 3:09:16 PM GMT
15:09:16.926 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.926 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.927 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:16.927 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:16.927 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:16.927 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:16.927 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
15:09:16.927 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
15:09:16.927 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
15:09:16.927 INFO TestIntervalTransformingWalker - Requester pays: disabled
15:09:16.927 INFO TestIntervalTransformingWalker - Initializing engine
15:09:16.928 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
15:09:16.928 INFO TestIntervalTransformingWalker - Done initializing engine
15:09:16.928 INFO ProgressMeter - Starting traversal
15:09:16.928 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.928 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.928 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.928 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 3:09:16 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:16.948 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.948 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:16.948 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:16.948 INFO TestIntervalTransformingWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:16.948 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:16.948 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 3:09:16 PM GMT
15:09:16.948 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.948 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.948 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:16.948 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:16.948 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:16.948 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:16.948 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
15:09:16.948 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
15:09:16.948 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
15:09:16.948 INFO TestIntervalTransformingWalker - Requester pays: disabled
15:09:16.949 INFO TestIntervalTransformingWalker - Initializing engine
15:09:16.949 INFO TestIntervalTransformingWalker - Done initializing engine
15:09:16.949 INFO ProgressMeter - Starting traversal
15:09:16.949 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.949 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.950 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.950 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 3:09:16 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:16.966 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.966 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:16.966 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:16.966 INFO TestIntervalTransformingWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:16.966 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:16.967 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 3:09:16 PM GMT
15:09:16.967 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.967 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
15:09:16.967 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:16.967 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:16.967 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:16.967 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:16.967 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
15:09:16.967 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
15:09:16.967 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
15:09:16.967 INFO TestIntervalTransformingWalker - Requester pays: disabled
15:09:16.967 INFO TestIntervalTransformingWalker - Initializing engine
15:09:16.967 INFO TestIntervalTransformingWalker - Done initializing engine
15:09:16.967 INFO ProgressMeter - Starting traversal
15:09:16.967 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.968 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.968 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.968 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 3:09:16 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:16.984 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:16.984 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:16.984 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:16.984 INFO TestIntervalWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:16.984 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:16.984 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 3:09:16 PM GMT
15:09:16.984 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:16.984 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:16.985 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:16.985 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:16.985 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:16.985 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:16.985 INFO TestIntervalWalker - Deflater: IntelDeflater
15:09:16.985 INFO TestIntervalWalker - Inflater: IntelInflater
15:09:16.985 INFO TestIntervalWalker - GCS max retries/reopens: 20
15:09:16.985 INFO TestIntervalWalker - Requester pays: disabled
15:09:16.985 INFO TestIntervalWalker - Initializing engine
15:09:16.986 INFO IntervalArgumentCollection - Processing 1 bp from intervals
15:09:16.986 INFO TestIntervalWalker - Done initializing engine
15:09:16.986 INFO ProgressMeter - Starting traversal
15:09:16.986 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:16.986 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:16.986 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:16.986 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 3:09:16 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:17.002 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.002 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:17.002 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:17.002 INFO TestIntervalWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:17.002 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:17.002 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 3:09:17 PM GMT
15:09:17.002 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.002 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.002 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:17.002 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:17.002 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:17.002 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:17.002 INFO TestIntervalWalker - Deflater: IntelDeflater
15:09:17.002 INFO TestIntervalWalker - Inflater: IntelInflater
15:09:17.002 INFO TestIntervalWalker - GCS max retries/reopens: 20
15:09:17.002 INFO TestIntervalWalker - Requester pays: disabled
15:09:17.002 INFO TestIntervalWalker - Initializing engine
15:09:17.003 INFO TestIntervalWalker - Done initializing engine
15:09:17.003 INFO ProgressMeter - Starting traversal
15:09:17.003 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:17.003 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:17.003 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:17.003 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 3:09:17 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:17.024 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.024 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:17.024 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:17.024 INFO TestIntervalWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:17.024 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:17.024 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 3:09:17 PM GMT
15:09:17.024 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.024 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.024 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:17.024 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:17.025 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:17.025 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:17.025 INFO TestIntervalWalker - Deflater: IntelDeflater
15:09:17.025 INFO TestIntervalWalker - Inflater: IntelInflater
15:09:17.025 INFO TestIntervalWalker - GCS max retries/reopens: 20
15:09:17.025 INFO TestIntervalWalker - Requester pays: disabled
15:09:17.025 INFO TestIntervalWalker - Initializing engine
15:09:17.025 INFO TestIntervalWalker - Done initializing engine
15:09:17.025 INFO ProgressMeter - Starting traversal
15:09:17.025 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:17.025 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:17.025 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:17.025 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 3:09:17 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:after_master_merge-284-g4157897-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
15:09:17.222 INFO FeatureManager - Using codec IntervalListCodec to read file file:///gatkCloneMountPoint/src/test/resources/picard_intervals.interval_list
15:09:17.224 INFO IntervalArgumentCollection - Processing 20 bp from intervals
15:09:17.224 INFO ProgressMeter - Starting traversal
15:09:17.224 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:17.224 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:17.224 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:17.238 INFO ProgressMeter - Starting traversal
15:09:17.238 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:17.239 INFO ProgressMeter - unmapped 0.0 0 NaN
15:09:17.239 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:17.257 INFO ProgressMeter - Starting traversal
15:09:17.258 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
15:09:17.314 INFO ProgressMeter - unmapped 0.0 0 0.0
15:09:17.314 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:17.330 INFO ProgressMeter - Starting traversal
15:09:17.330 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:17.346 INFO ProgressMeter - unmapped 0.0 0 0.0
15:09:17.346 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:09:17.361 INFO ProgressMeter - Starting traversal
15:09:17.361 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
15:09:17.389 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.389 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:17.389 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:17.389 INFO TestIntervalWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:17.389 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:17.389 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 3:09:17 PM GMT
15:09:17.389 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.389 INFO TestIntervalWalker - ------------------------------------------------------------
15:09:17.389 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:17.389 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:17.390 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:17.390 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:17.390 INFO TestIntervalWalker - Deflater: IntelDeflater
15:09:17.390 INFO TestIntervalWalker - Inflater: IntelInflater
15:09:17.390 INFO TestIntervalWalker - GCS max retries/reopens: 20
15:09:17.390 INFO TestIntervalWalker - Requester pays: disabled
15:09:17.390 INFO TestIntervalWalker - Initializing engine
15:09:17.390 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 3:09:17 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976