20:13:37.369 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
20:13:37.396 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
20:13:37.476 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:13:37.479 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:13:37.480 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:13:37.484 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:13:37.485 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:13:37.489 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:13:37.509 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
20:13:37.516 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:13:37.521 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
20:13:37.525 INFO ProgressMeter - Starting traversal
20:13:37.525 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.525 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.525 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.557 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:13:37.557 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.557 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.558 INFO TestGATKToolWithFeatures - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.558 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.558 INFO TestGATKToolWithFeatures - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.558 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:13:37.558 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:13:37.558 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.558 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.558 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.558 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.559 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:13:37.559 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:13:37.559 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:13:37.559 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:13:37.559 INFO TestGATKToolWithFeatures - Initializing engine
20:13:37.560 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
20:13:37.562 INFO TestGATKToolWithFeatures - Done initializing engine
20:13:37.562 INFO ProgressMeter - Starting traversal
20:13:37.562 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.562 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.562 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.562 INFO TestGATKToolWithFeatures - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.578 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.578 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.578 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.578 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.579 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.579 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.579 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.579 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.579 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.579 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.579 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.579 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.579 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:13:37.579 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:13:37.579 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:13:37.579 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:13:37.579 INFO TestIntervalTransformingWalker - Initializing engine
20:13:37.580 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:13:37.581 INFO TestIntervalTransformingWalker - Done initializing engine
20:13:37.581 INFO ProgressMeter - Starting traversal
20:13:37.581 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.582 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.582 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.582 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.586 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.586 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.587 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.587 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.587 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.587 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.587 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.587 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.587 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.587 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.587 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.587 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.587 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:13:37.587 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:13:37.587 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:13:37.587 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:13:37.587 INFO TestIntervalTransformingWalker - Initializing engine
20:13:37.588 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
20:13:37.588 INFO TestIntervalTransformingWalker - Done initializing engine
20:13:37.588 INFO ProgressMeter - Starting traversal
20:13:37.588 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.589 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.589 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.589 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.593 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.593 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.594 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.594 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.594 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.594 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.594 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.594 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.594 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.594 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.594 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.594 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.594 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:13:37.594 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:13:37.594 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:13:37.594 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:13:37.594 INFO TestIntervalTransformingWalker - Initializing engine
20:13:37.595 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
20:13:37.595 INFO TestIntervalTransformingWalker - Done initializing engine
20:13:37.595 INFO ProgressMeter - Starting traversal
20:13:37.595 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.595 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.595 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.595 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.599 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.599 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.599 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.599 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.599 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.599 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.599 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.599 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.599 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.599 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.599 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.599 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.600 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:13:37.600 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:13:37.600 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:13:37.600 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:13:37.600 INFO TestIntervalTransformingWalker - Initializing engine
20:13:37.600 INFO TestIntervalTransformingWalker - Done initializing engine
20:13:37.600 INFO ProgressMeter - Starting traversal
20:13:37.600 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.600 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.600 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.600 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.605 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.605 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.605 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.605 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.605 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.605 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.605 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.605 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:13:37.605 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.605 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.605 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.605 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.605 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:13:37.605 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:13:37.605 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:13:37.605 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:13:37.605 INFO TestIntervalTransformingWalker - Initializing engine
20:13:37.605 INFO TestIntervalTransformingWalker - Done initializing engine
20:13:37.606 INFO ProgressMeter - Starting traversal
20:13:37.606 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.606 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.606 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.606 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.616 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.616 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.616 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.616 INFO TestIntervalWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.616 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.616 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.616 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.616 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.617 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.617 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.617 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.617 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.617 INFO TestIntervalWalker - Deflater: IntelDeflater
20:13:37.617 INFO TestIntervalWalker - Inflater: IntelInflater
20:13:37.617 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:13:37.617 INFO TestIntervalWalker - Requester pays: disabled
20:13:37.617 INFO TestIntervalWalker - Initializing engine
20:13:37.618 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:13:37.618 INFO TestIntervalWalker - Done initializing engine
20:13:37.618 INFO ProgressMeter - Starting traversal
20:13:37.618 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.618 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.618 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.618 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.624 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.625 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.625 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.625 INFO TestIntervalWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.625 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.625 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.625 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.625 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.625 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.625 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.625 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.625 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.625 INFO TestIntervalWalker - Deflater: IntelDeflater
20:13:37.625 INFO TestIntervalWalker - Inflater: IntelInflater
20:13:37.625 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:13:37.625 INFO TestIntervalWalker - Requester pays: disabled
20:13:37.626 INFO TestIntervalWalker - Initializing engine
20:13:37.626 INFO TestIntervalWalker - Done initializing engine
20:13:37.626 INFO ProgressMeter - Starting traversal
20:13:37.626 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.626 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.626 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.626 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:37.631 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.631 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.631 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.631 INFO TestIntervalWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.631 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.631 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.631 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.631 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.631 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.632 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.632 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.632 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.632 INFO TestIntervalWalker - Deflater: IntelDeflater
20:13:37.632 INFO TestIntervalWalker - Inflater: IntelInflater
20:13:37.632 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:13:37.632 INFO TestIntervalWalker - Requester pays: disabled
20:13:37.632 INFO TestIntervalWalker - Initializing engine
20:13:37.632 INFO TestIntervalWalker - Done initializing engine
20:13:37.632 INFO ProgressMeter - Starting traversal
20:13:37.632 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.632 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.632 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.632 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
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
20:13:37.676 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/picard_intervals.interval_list
20:13:37.678 INFO IntervalArgumentCollection - Processing 20 bp from intervals
20:13:37.679 INFO ProgressMeter - Starting traversal
20:13:37.679 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.679 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.679 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.683 INFO ProgressMeter - Starting traversal
20:13:37.683 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.683 INFO ProgressMeter - unmapped 0.0 0 NaN
20:13:37.683 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.692 INFO ProgressMeter - Starting traversal
20:13:37.692 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
20:13:37.748 INFO ProgressMeter - unmapped 0.0 0 0.0
20:13:37.748 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.757 INFO ProgressMeter - Starting traversal
20:13:37.757 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.777 INFO ProgressMeter - unmapped 0.0 0 0.0
20:13:37.777 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:13:37.784 INFO ProgressMeter - Starting traversal
20:13:37.785 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:13:37.803 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.803 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:37.803 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:37.803 INFO TestIntervalWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:37.803 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:37.803 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:13:37 PM UTC
20:13:37.803 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.803 INFO TestIntervalWalker - ------------------------------------------------------------
20:13:37.804 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:37.804 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:37.804 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:37.804 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:37.804 INFO TestIntervalWalker - Deflater: IntelDeflater
20:13:37.804 INFO TestIntervalWalker - Inflater: IntelInflater
20:13:37.804 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:13:37.804 INFO TestIntervalWalker - Requester pays: disabled
20:13:37.804 INFO TestIntervalWalker - Initializing engine
20:13:37.804 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:13:37 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416