14:51:04.135 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
14:51:04.160 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
14:51:04.277 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
14:51:04.281 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
14:51:04.283 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
14:51:04.287 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
14:51:04.289 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
14:51:04.293 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
14:51:04.316 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
14:51:04.324 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
14:51:04.330 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
14:51:04.334 INFO ProgressMeter - Starting traversal
14:51:04.334 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.334 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.335 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.378 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:51:04.378 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.378 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.378 INFO TestGATKToolWithFeatures - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.378 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.379 INFO TestGATKToolWithFeatures - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.379 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:51:04.379 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:51:04.379 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.379 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.379 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.379 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.379 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
14:51:04.379 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
14:51:04.380 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
14:51:04.380 INFO TestGATKToolWithFeatures - Requester pays: disabled
14:51:04.380 INFO TestGATKToolWithFeatures - Initializing engine
14:51:04.381 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
14:51:04.382 INFO TestGATKToolWithFeatures - Done initializing engine
14:51:04.382 INFO ProgressMeter - Starting traversal
14:51:04.382 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.382 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.382 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.382 INFO TestGATKToolWithFeatures - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.405 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.405 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.405 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.405 INFO TestIntervalTransformingWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.405 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.405 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.405 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.405 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.406 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.406 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.406 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.406 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.406 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
14:51:04.406 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
14:51:04.406 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
14:51:04.406 INFO TestIntervalTransformingWalker - Requester pays: disabled
14:51:04.406 INFO TestIntervalTransformingWalker - Initializing engine
14:51:04.407 INFO IntervalArgumentCollection - Processing 1 bp from intervals
14:51:04.409 INFO TestIntervalTransformingWalker - Done initializing engine
14:51:04.409 INFO ProgressMeter - Starting traversal
14:51:04.409 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.409 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.409 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.409 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.415 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.415 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.415 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.415 INFO TestIntervalTransformingWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.415 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.416 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.416 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.416 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.416 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.416 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.416 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.416 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.416 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
14:51:04.416 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
14:51:04.416 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
14:51:04.417 INFO TestIntervalTransformingWalker - Requester pays: disabled
14:51:04.417 INFO TestIntervalTransformingWalker - Initializing engine
14:51:04.417 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
14:51:04.418 INFO TestIntervalTransformingWalker - Done initializing engine
14:51:04.418 INFO ProgressMeter - Starting traversal
14:51:04.418 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.418 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.418 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.418 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.424 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.424 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.425 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.425 INFO TestIntervalTransformingWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.425 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.425 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.425 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.425 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.425 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.425 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.425 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.425 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.425 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
14:51:04.425 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
14:51:04.425 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
14:51:04.425 INFO TestIntervalTransformingWalker - Requester pays: disabled
14:51:04.426 INFO TestIntervalTransformingWalker - Initializing engine
14:51:04.426 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
14:51:04.427 INFO TestIntervalTransformingWalker - Done initializing engine
14:51:04.427 INFO ProgressMeter - Starting traversal
14:51:04.427 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.427 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.427 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.427 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.434 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.434 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.434 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.434 INFO TestIntervalTransformingWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.434 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.434 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.434 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.434 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.434 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.434 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.434 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.434 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.434 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
14:51:04.435 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
14:51:04.435 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
14:51:04.435 INFO TestIntervalTransformingWalker - Requester pays: disabled
14:51:04.435 INFO TestIntervalTransformingWalker - Initializing engine
14:51:04.435 INFO TestIntervalTransformingWalker - Done initializing engine
14:51:04.435 INFO ProgressMeter - Starting traversal
14:51:04.435 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.436 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.436 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.436 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.442 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.442 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.442 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.442 INFO TestIntervalTransformingWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.443 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.443 INFO TestIntervalTransformingWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.443 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.443 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
14:51:04.443 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.443 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.443 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.443 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.443 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
14:51:04.443 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
14:51:04.443 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
14:51:04.443 INFO TestIntervalTransformingWalker - Requester pays: disabled
14:51:04.443 INFO TestIntervalTransformingWalker - Initializing engine
14:51:04.444 INFO TestIntervalTransformingWalker - Done initializing engine
14:51:04.444 INFO ProgressMeter - Starting traversal
14:51:04.444 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.444 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.444 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.444 INFO TestIntervalTransformingWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.450 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.450 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.450 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.450 INFO TestIntervalWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.450 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.450 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.451 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.451 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.451 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.451 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.451 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.451 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.451 INFO TestIntervalWalker - Deflater: IntelDeflater
14:51:04.451 INFO TestIntervalWalker - Inflater: IntelInflater
14:51:04.451 INFO TestIntervalWalker - GCS max retries/reopens: 20
14:51:04.451 INFO TestIntervalWalker - Requester pays: disabled
14:51:04.451 INFO TestIntervalWalker - Initializing engine
14:51:04.452 INFO IntervalArgumentCollection - Processing 1 bp from intervals
14:51:04.452 INFO TestIntervalWalker - Done initializing engine
14:51:04.452 INFO ProgressMeter - Starting traversal
14:51:04.452 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.452 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.453 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.453 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.458 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.458 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.458 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.458 INFO TestIntervalWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.458 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.459 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.459 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.459 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.459 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.459 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.459 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.459 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.459 INFO TestIntervalWalker - Deflater: IntelDeflater
14:51:04.459 INFO TestIntervalWalker - Inflater: IntelInflater
14:51:04.459 INFO TestIntervalWalker - GCS max retries/reopens: 20
14:51:04.459 INFO TestIntervalWalker - Requester pays: disabled
14:51:04.459 INFO TestIntervalWalker - Initializing engine
14:51:04.460 INFO TestIntervalWalker - Done initializing engine
14:51:04.460 INFO ProgressMeter - Starting traversal
14:51:04.460 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.460 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.460 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.460 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:04.466 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.466 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.466 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.466 INFO TestIntervalWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.466 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.466 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.466 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.466 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.467 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.467 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.467 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.467 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.467 INFO TestIntervalWalker - Deflater: IntelDeflater
14:51:04.467 INFO TestIntervalWalker - Inflater: IntelInflater
14:51:04.467 INFO TestIntervalWalker - GCS max retries/reopens: 20
14:51:04.467 INFO TestIntervalWalker - Requester pays: disabled
14:51:04.467 INFO TestIntervalWalker - Initializing engine
14:51:04.467 INFO TestIntervalWalker - Done initializing engine
14:51:04.467 INFO ProgressMeter - Starting traversal
14:51:04.467 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.467 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.467 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.467 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:null
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
14:51:04.519 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/picard_intervals.interval_list
14:51:04.521 INFO IntervalArgumentCollection - Processing 20 bp from intervals
14:51:04.522 INFO ProgressMeter - Starting traversal
14:51:04.522 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.522 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.522 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.527 INFO ProgressMeter - Starting traversal
14:51:04.527 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.527 INFO ProgressMeter - unmapped 0.0 0 NaN
14:51:04.527 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.538 INFO ProgressMeter - Starting traversal
14:51:04.538 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
14:51:04.595 INFO ProgressMeter - unmapped 0.0 0 0.0
14:51:04.595 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.602 INFO ProgressMeter - Starting traversal
14:51:04.602 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.618 INFO ProgressMeter - unmapped 0.0 0 0.0
14:51:04.618 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:51:04.624 INFO ProgressMeter - Starting traversal
14:51:04.624 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:51:04.644 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.644 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:04.645 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:04.645 INFO TestIntervalWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:04.645 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:04.645 INFO TestIntervalWalker - Start Date/Time: March 4, 2026 at 2:51:04 PM UTC
14:51:04.645 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.645 INFO TestIntervalWalker - ------------------------------------------------------------
14:51:04.645 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:04.645 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:04.645 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:04.645 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:04.645 INFO TestIntervalWalker - Deflater: IntelDeflater
14:51:04.645 INFO TestIntervalWalker - Inflater: IntelInflater
14:51:04.645 INFO TestIntervalWalker - GCS max retries/reopens: 20
14:51:04.645 INFO TestIntervalWalker - Requester pays: disabled
14:51:04.646 INFO TestIntervalWalker - Initializing engine
14:51:04.646 INFO TestIntervalWalker - Shutting down engine
[March 4, 2026 at 2:51:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600