18:46:03.789 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
18:46:03.807 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
18:46:03.884 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
18:46:03.888 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
18:46:03.890 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
18:46:03.894 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
18:46:03.895 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
18:46:03.899 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
18:46:03.923 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
18:46:03.929 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
18:46:03.934 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
18:46:03.938 INFO ProgressMeter - Starting traversal
18:46:03.938 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:03.939 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:03.939 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:03.976 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:46:03.976 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
18:46:03.976 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:03.976 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:03.976 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:03.976 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 6:46:03 PM UTC
18:46:03.976 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:46:03.976 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:46:03.977 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:03.977 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:03.977 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:03.977 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:03.977 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
18:46:03.977 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
18:46:03.977 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
18:46:03.977 INFO TestGATKToolWithFeatures - Requester pays: disabled
18:46:03.977 INFO TestGATKToolWithFeatures - Initializing engine
18:46:03.978 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
18:46:03.980 INFO TestGATKToolWithFeatures - Done initializing engine
18:46:03.980 INFO ProgressMeter - Starting traversal
18:46:03.980 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:03.980 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:03.980 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:03.980 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 6:46:03 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:03.998 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:03.998 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:03.998 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:03.998 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:03.998 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:03.999 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 6:46:03 PM UTC
18:46:03.999 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:03.999 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:03.999 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:03.999 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:03.999 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:03.999 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:03.999 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
18:46:03.999 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
18:46:03.999 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
18:46:03.999 INFO TestIntervalTransformingWalker - Requester pays: disabled
18:46:03.999 INFO TestIntervalTransformingWalker - Initializing engine
18:46:04.000 INFO IntervalArgumentCollection - Processing 1 bp from intervals
18:46:04.001 INFO TestIntervalTransformingWalker - Done initializing engine
18:46:04.001 INFO ProgressMeter - Starting traversal
18:46:04.002 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.002 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.002 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.002 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.007 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.007 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.007 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.007 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.007 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.007 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.007 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.007 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.008 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.008 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.008 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.008 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.008 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
18:46:04.008 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
18:46:04.008 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
18:46:04.008 INFO TestIntervalTransformingWalker - Requester pays: disabled
18:46:04.008 INFO TestIntervalTransformingWalker - Initializing engine
18:46:04.009 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
18:46:04.009 INFO TestIntervalTransformingWalker - Done initializing engine
18:46:04.009 INFO ProgressMeter - Starting traversal
18:46:04.009 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.009 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.009 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.009 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.014 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.014 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.014 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.015 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.015 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.015 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.015 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.015 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.015 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.015 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.015 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.015 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.015 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
18:46:04.015 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
18:46:04.015 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
18:46:04.015 INFO TestIntervalTransformingWalker - Requester pays: disabled
18:46:04.015 INFO TestIntervalTransformingWalker - Initializing engine
18:46:04.016 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
18:46:04.016 INFO TestIntervalTransformingWalker - Done initializing engine
18:46:04.016 INFO ProgressMeter - Starting traversal
18:46:04.016 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.016 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.016 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.016 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.022 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.022 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.022 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.022 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.022 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.022 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.022 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.022 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.022 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.022 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.023 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.023 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.023 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
18:46:04.023 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
18:46:04.023 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
18:46:04.023 INFO TestIntervalTransformingWalker - Requester pays: disabled
18:46:04.023 INFO TestIntervalTransformingWalker - Initializing engine
18:46:04.023 INFO TestIntervalTransformingWalker - Done initializing engine
18:46:04.023 INFO ProgressMeter - Starting traversal
18:46:04.024 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.024 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.024 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.024 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.029 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.029 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.029 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.029 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.029 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.029 INFO TestIntervalTransformingWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.029 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.029 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
18:46:04.029 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.029 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.029 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.029 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.029 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
18:46:04.029 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
18:46:04.030 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
18:46:04.030 INFO TestIntervalTransformingWalker - Requester pays: disabled
18:46:04.030 INFO TestIntervalTransformingWalker - Initializing engine
18:46:04.030 INFO TestIntervalTransformingWalker - Done initializing engine
18:46:04.030 INFO ProgressMeter - Starting traversal
18:46:04.030 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.030 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.030 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.030 INFO TestIntervalTransformingWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.035 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.035 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.035 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.035 INFO TestIntervalWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.035 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.035 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.035 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.035 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.036 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.036 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.036 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.036 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.036 INFO TestIntervalWalker - Deflater: IntelDeflater
18:46:04.036 INFO TestIntervalWalker - Inflater: IntelInflater
18:46:04.036 INFO TestIntervalWalker - GCS max retries/reopens: 20
18:46:04.036 INFO TestIntervalWalker - Requester pays: disabled
18:46:04.036 INFO TestIntervalWalker - Initializing engine
18:46:04.037 INFO IntervalArgumentCollection - Processing 1 bp from intervals
18:46:04.037 INFO TestIntervalWalker - Done initializing engine
18:46:04.037 INFO ProgressMeter - Starting traversal
18:46:04.037 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.037 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.037 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.037 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.041 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.041 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.041 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.041 INFO TestIntervalWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.041 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.041 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.042 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.042 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.042 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.042 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.042 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.042 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.042 INFO TestIntervalWalker - Deflater: IntelDeflater
18:46:04.042 INFO TestIntervalWalker - Inflater: IntelInflater
18:46:04.042 INFO TestIntervalWalker - GCS max retries/reopens: 20
18:46:04.042 INFO TestIntervalWalker - Requester pays: disabled
18:46:04.042 INFO TestIntervalWalker - Initializing engine
18:46:04.043 INFO TestIntervalWalker - Done initializing engine
18:46:04.043 INFO ProgressMeter - Starting traversal
18:46:04.043 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.043 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.043 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.043 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.048 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.048 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.048 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.048 INFO TestIntervalWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.048 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.048 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.048 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.048 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.049 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.049 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.049 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.049 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.049 INFO TestIntervalWalker - Deflater: IntelDeflater
18:46:04.049 INFO TestIntervalWalker - Inflater: IntelInflater
18:46:04.049 INFO TestIntervalWalker - GCS max retries/reopens: 20
18:46:04.049 INFO TestIntervalWalker - Requester pays: disabled
18:46:04.049 INFO TestIntervalWalker - Initializing engine
18:46:04.049 INFO TestIntervalWalker - Done initializing engine
18:46:04.049 INFO ProgressMeter - Starting traversal
18:46:04.049 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.049 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.049 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.049 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 6:46:04 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
18:46:04.096 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/picard_intervals.interval_list
18:46:04.098 INFO IntervalArgumentCollection - Processing 20 bp from intervals
18:46:04.098 INFO ProgressMeter - Starting traversal
18:46:04.098 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.099 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.099 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.102 INFO ProgressMeter - Starting traversal
18:46:04.102 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.103 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.103 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.113 INFO ProgressMeter - Starting traversal
18:46:04.113 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
18:46:04.172 INFO ProgressMeter - unmapped 0.0 0 0.0
18:46:04.172 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.181 INFO ProgressMeter - Starting traversal
18:46:04.181 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.197 INFO ProgressMeter - unmapped 0.0 0 0.0
18:46:04.197 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:46:04.204 INFO ProgressMeter - Starting traversal
18:46:04.204 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
18:46:04.222 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.222 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.222 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.222 INFO TestIntervalWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.222 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.222 INFO TestIntervalWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.222 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.222 INFO TestIntervalWalker - ------------------------------------------------------------
18:46:04.222 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.222 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.222 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.223 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.223 INFO TestIntervalWalker - Deflater: IntelDeflater
18:46:04.223 INFO TestIntervalWalker - Inflater: IntelInflater
18:46:04.223 INFO TestIntervalWalker - GCS max retries/reopens: 20
18:46:04.223 INFO TestIntervalWalker - Requester pays: disabled
18:46:04.223 INFO TestIntervalWalker - Initializing engine
18:46:04.223 INFO TestIntervalWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600