20:47:48.189 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
20:47:48.255 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
20:47:48.567 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:47:48.571 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:47:48.573 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:47:48.577 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:47:48.579 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:47:48.583 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:47:48.619 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
20:47:48.646 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:47:48.662 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
20:47:48.666 INFO ProgressMeter - Starting traversal
20:47:48.666 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.666 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.666 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.786 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:47:48.786 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.786 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.786 INFO TestGATKToolWithFeatures - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.786 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.787 INFO TestGATKToolWithFeatures - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.787 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:47:48.787 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:47:48.787 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.787 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.787 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.787 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.787 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:47:48.787 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:47:48.787 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:47:48.787 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:47:48.787 INFO TestGATKToolWithFeatures - Initializing engine
20:47:48.789 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
20:47:48.790 INFO TestGATKToolWithFeatures - Done initializing engine
20:47:48.791 INFO ProgressMeter - Starting traversal
20:47:48.791 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.791 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.791 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.791 INFO TestGATKToolWithFeatures - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.839 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.839 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.839 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.840 INFO TestIntervalTransformingWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.840 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.840 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.840 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.840 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.840 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.840 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.840 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.840 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.840 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:47:48.840 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:47:48.840 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:47:48.840 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:47:48.841 INFO TestIntervalTransformingWalker - Initializing engine
20:47:48.841 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:47:48.843 INFO TestIntervalTransformingWalker - Done initializing engine
20:47:48.843 INFO ProgressMeter - Starting traversal
20:47:48.843 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.843 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.843 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.843 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.859 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.859 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.859 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.859 INFO TestIntervalTransformingWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.859 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.859 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.859 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.859 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.859 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.859 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.859 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.860 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.860 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:47:48.860 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:47:48.860 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:47:48.860 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:47:48.860 INFO TestIntervalTransformingWalker - Initializing engine
20:47:48.861 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
20:47:48.861 INFO TestIntervalTransformingWalker - Done initializing engine
20:47:48.861 INFO ProgressMeter - Starting traversal
20:47:48.861 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.861 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.861 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.861 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.877 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.877 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.877 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.877 INFO TestIntervalTransformingWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.877 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.877 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.877 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.877 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.877 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.877 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.877 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.877 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.877 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:47:48.877 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:47:48.877 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:47:48.878 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:47:48.878 INFO TestIntervalTransformingWalker - Initializing engine
20:47:48.878 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
20:47:48.879 INFO TestIntervalTransformingWalker - Done initializing engine
20:47:48.879 INFO ProgressMeter - Starting traversal
20:47:48.879 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.879 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.879 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.879 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.894 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.894 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.894 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.894 INFO TestIntervalTransformingWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.894 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.894 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.894 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.894 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.894 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.894 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.894 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.894 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.894 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:47:48.895 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:47:48.895 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:47:48.895 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:47:48.895 INFO TestIntervalTransformingWalker - Initializing engine
20:47:48.895 INFO TestIntervalTransformingWalker - Done initializing engine
20:47:48.895 INFO ProgressMeter - Starting traversal
20:47:48.895 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.896 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.896 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.896 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.912 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.912 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.912 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.912 INFO TestIntervalTransformingWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.912 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.912 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.912 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.912 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:47:48.912 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.912 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.912 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.912 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.912 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:47:48.912 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:47:48.912 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:47:48.913 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:47:48.913 INFO TestIntervalTransformingWalker - Initializing engine
20:47:48.913 INFO TestIntervalTransformingWalker - Done initializing engine
20:47:48.913 INFO ProgressMeter - Starting traversal
20:47:48.913 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.913 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.913 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.913 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.930 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.930 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.930 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.930 INFO TestIntervalWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.930 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.930 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.931 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.931 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.931 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.931 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.931 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.931 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.931 INFO TestIntervalWalker - Deflater: IntelDeflater
20:47:48.931 INFO TestIntervalWalker - Inflater: IntelInflater
20:47:48.931 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:47:48.931 INFO TestIntervalWalker - Requester pays: disabled
20:47:48.931 INFO TestIntervalWalker - Initializing engine
20:47:48.932 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:47:48.932 INFO TestIntervalWalker - Done initializing engine
20:47:48.932 INFO ProgressMeter - Starting traversal
20:47:48.932 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.933 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.933 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.933 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.948 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.948 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.948 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.948 INFO TestIntervalWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.948 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.948 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.948 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.949 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.949 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.949 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.949 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.949 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.949 INFO TestIntervalWalker - Deflater: IntelDeflater
20:47:48.949 INFO TestIntervalWalker - Inflater: IntelInflater
20:47:48.949 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:47:48.949 INFO TestIntervalWalker - Requester pays: disabled
20:47:48.949 INFO TestIntervalWalker - Initializing engine
20:47:48.950 INFO TestIntervalWalker - Done initializing engine
20:47:48.950 INFO ProgressMeter - Starting traversal
20:47:48.950 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.950 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.950 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.950 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:48.966 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.966 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:48.966 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:48.966 INFO TestIntervalWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:48.966 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:48.966 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:47:48 PM GMT
20:47:48.966 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.966 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:48.966 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:48.966 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:48.966 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:48.966 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:48.967 INFO TestIntervalWalker - Deflater: IntelDeflater
20:47:48.967 INFO TestIntervalWalker - Inflater: IntelInflater
20:47:48.967 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:47:48.967 INFO TestIntervalWalker - Requester pays: disabled
20:47:48.967 INFO TestIntervalWalker - Initializing engine
20:47:48.967 INFO TestIntervalWalker - Done initializing engine
20:47:48.967 INFO ProgressMeter - Starting traversal
20:47:48.967 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:48.967 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:48.967 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:48.967 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:47:48 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:4.6.2.0-13-g9eb1b78-SNAPSHOT
Optional Arguments:
--add-output-sam-program-record <Boolean>
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}
--add-output-vcf-command-line <Boolean>
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}
--annotation,-A <String> One or more specific annotations to add to variant calls This argument may be specified 0
or more times. Default value: null. Possible values: {AlleleFraction, AllelePseudoDepth,
AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
AS_StrandBiasMutectAnnotation, AS_StrandOddsRatio, AssemblyComplexity, BaseQuality,
BaseQualityHistogram, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest,
CountNs, Coverage, CycleSkipStatus, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet,
FisherStrand, FragmentDepthPerAlleleBySample, FragmentLength, GcContent,
GenotypeSummaries, HaplotypeFilteringAnnotation, HmerIndelLength, HmerIndelNuc,
HmerMotifs, InbreedingCoeff, IndelClassify, IndelLength, LikelihoodRankSumTest,
MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts,
OriginalAlignment, PossibleDeNovo, QualByDepth, RawGtCount, ReadPosition,
ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample,
StrandOddsRatio, TandemRepeat, TransmittedSingleton, UniqueAltReadCount, VariantType}
--annotation-group,-G <String>One or more groups of annotations to apply to variant calls This argument may be
specified 0 or more times. Default value: null. Possible values:
{AlleleSpecificAnnotation, AS_StandardAnnotation, GenotypeAnnotation, InfoFieldAnnotation,
JumboGenotypeAnnotation, JumboInfoAnnotation, ReducibleAnnotation, StandardAnnotation,
StandardFlowBasedAnnotation, StandardHCAnnotation, StandardMutectAnnotation,
VariantAnnotation}
--annotations-to-exclude,-AX <String>
One or more specific annotations to exclude from variant calls This argument may be
specified 0 or more times. Default value: null. Any value allowed
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--cloud-index-prefetch-buffer,-CIPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
cloudPrefetchBuffer if unset. Default value: -1.
--cloud-prefetch-buffer,-CPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
--create-output-bam-index,-OBI <Boolean>
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}
--create-output-bam-md5,-OBM <Boolean>
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}
--create-output-variant-index,-OVI <Boolean>
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}
--create-output-variant-md5,-OVM <Boolean>
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}
--disable-bam-index-caching,-DBIC <Boolean>
If true, don't cache bam indexes, this will reduce memory requirements but may harm
performance if many intervals are specified. Caching is automatically disabled if there
are no intervals specified. Default value: false. Possible values: {true, false}
--disable-read-filter,-DF <String>
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {WellformedReadFilter}
--disable-sequence-dictionary-validation <Boolean>
If specified, do not check the sequence dictionaries from our inputs for compatibility.
Use at your own risk! Default value: false. Possible values: {true, false}
--exclude-intervals,-XL <String>
One or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.
--flow-order-for-annotations <String>
flow order used for this annotations. [readGroup:]flowOrder This argument may be
specified 0 or more times. Default value: null.
--founder-id <String> Samples representing the population "founders" This argument may be specified 0 or more
times. Default value: null.
--gatk-config-file <String> A configuration file to use with the GATK. Default value: null.
--gcs-max-retries,-gcs-retries <Integer>
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.
--gcs-project-for-requester-pays <String>
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. User must have storage.buckets.get permission on the bucket being accessed.
Default value: .
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--input,-I <GATKPath> BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
Default value: null.
--interval-exclusion-padding,-ixp <Integer>
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
--interval-merging-rule,-imr <IntervalMergingRule>
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}
--interval-padding,-ip <Integer>
Amount of padding (in bp) to add to each interval you are including. Default value: 0.
--interval-set-rule,-isr <IntervalSetRule>
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}
--intervals,-L <String> One or more genomic intervals over which to operate This argument may be specified 0 or
more times. Default value: null.
--inverted-read-filter,-XRF <String>
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis
(after regular read filters). This argument may be specified 0 or more times. Default
value: null.
--lenient,-LE <Boolean> Lenient processing of VCF files Default value: false. Possible values: {true, false}
--max-variants-per-shard <Integer>
If non-zero, partitions VCF output into shards, each containing up to the given number of
records. Default value: 0.
--output,-out <File> Input variants Default value: null.
--pedigree,-ped <GATKPath> Pedigree file for determining the population "founders" Default value: null.
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--read-filter,-RF <String> Read filters to be applied before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {AlignmentAgreesWithHeaderReadFilter,
AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
ExcessiveEndClippedReadFilter, FirstOfPairReadFilter,
FlowBasedTPAttributeSymetricReadFilter, FlowBasedTPAttributeValidReadFilter,
FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter,
HmerQualitySymetricReadFilter, IntervalOverlapReadFilter,
JexlExpressionReadTagValueFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupHasFlowOrderReadFilter,
ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter,
ReadNameReadFilter, ReadStrandFilter, ReadTagValueFilter, SampleReadFilter,
SecondOfPairReadFilter, SeqIsStoredReadFilter, SoftClippedReadFilter,
ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedFlowBasedReadFilter,
WellformedReadFilter}
--read-index <GATKPath> Indices to use for the read inputs. If specified, an index must be provided for every read
input and in the same order as the read inputs. If this argument is not specified, the
path to the index for each input will be inferred automatically. This argument may be
specified 0 or more times. Default value: null.
--read-validation-stringency,-VS <ValidationStringency>
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default
stringency value SILENT can improve performance when processing a BAM file in which
variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default
value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
--reference,-R <GATKPath> Reference sequence Default value: null.
--seconds-between-progress-updates <Double>
Output traversal statistics every time this many seconds elapse Default value: 10.0.
--sequence-dictionary <GATKPath>
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.
--sites-only-vcf-output <Boolean>
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}
--tmp-dir <GATKPath> Temp directory to use. Default value: null.
--use-jdk-deflater,-jdk-deflater <Boolean>
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}
--use-jdk-inflater,-jdk-inflater <Boolean>
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}
--verbosity <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--disable-tool-default-annotations <Boolean>
Disable all tool default annotations Default value: false. Possible values: {true, false}
--disable-tool-default-read-filters <Boolean>
Disable all tool default read filters (WARNING: many tools will not function correctly
without their default read filters on) Default value: false. Possible values: {true,
false}
--enable-all-annotations <Boolean>
Use all possible annotations (not for the faint of heart) Default value: false. Possible
values: {true, false}
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
Conditional Arguments for annotation:
Valid only if "AllelePseudoDepth" is specified:
--dirichlet-keep-prior-in-count <Boolean>
By default we don't keep the prior use in the output counts ase it makes it easier to
interpretthis quantity as the number of supporting reads specially in low depth sites. We
this toggled the prior is included Default value: false. Possible values: {true, false}
--dirichlet-prior-pseudo-count <Double>
Pseudo-count used as prior for all alleles. The default is 1.0 resulting in a flat prior
Default value: 1.0.
--pseudo-count-weight-decay-rate <Double>
A what rate the weight of a read decreases base on its informativeness; e.g. 1.0 is linear
decay (default), 2.0 is for quadratic decay Default value: 1.0.
Valid only if "AssemblyComplexity" is specified:
--assembly-complexity-reference-mode <Boolean>
If enabled will treat the reference as the basis for assembly complexity as opposed to
estimated germline haplotypes Default value: false. Possible values: {true, false}
Valid only if "PossibleDeNovo" is specified:
--denovo-depth-threshold <Integer>
Minimum depth (DP) for all trio members to be considered for de novo calculation. Default
value: 0.
--denovo-parent-gq-threshold <Integer>
Minimum genotype quality for parents to be considered for de novo calculation (separate
from GQ thershold for full trio). Default value: 20.
Valid only if "RMSMappingQuality" is specified:
--allow-old-rms-mapping-quality-annotation-data <Boolean>
Override to allow old RMSMappingQuality annotated VCFs to function Default value: false.
Possible values: {true, false}
Conditional Arguments for readFilter:
Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases <Integer>Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
overrides threshold fraction. Default value: null. Cannot be used in conjunction with
argument(s) maxAmbiguousBaseFraction
--ambig-filter-frac <Double> Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjunction
with argument(s) maxAmbiguousBases
Valid only if "ExcessiveEndClippedReadFilter" is specified:
--max-clipped-bases <Integer> Maximum number of clipped bases on either end of a given read Default value: 1000.
Valid only if "FlowBasedTPAttributeValidReadFilter" is specified:
--read-filter-max-hmer <Integer>
maxHmer to use for testing in the filter Default value: 12.
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length <Integer>
Maximum length of fragment (insert size) Default value: 1000000.
--min-fragment-length <Integer>
Minimum length of fragment (insert size) Default value: 0.
Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals <String> One or more genomic intervals to keep This argument must be specified at least once.
Required.
Valid only if "JexlExpressionReadTagValueFilter" is specified:
--read-filter-expression <String>
One or more JEXL expressions used to filter This argument must be specified at least
once. Required.
Valid only if "LibraryReadFilter" is specified:
--library <String> Name of the library to keep This argument must be specified at least once. Required.
Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality <Integer>
Maximum mapping quality to keep (inclusive) Default value: null.
--minimum-mapping-quality <Integer>
Minimum mapping quality to keep (inclusive) Default value: 10.
Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length <Integer>
Minimum start location difference at which mapped mates are considered distant Default
value: 1000.
Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends <Boolean>
Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
block Default value: false. Possible values: {true, false}
--filter-too-short <Integer> Minimum number of aligned bases Default value: 30.
Valid only if "PlatformReadFilter" is specified:
--platform-filter-name <String>
Platform attribute (PL) to match This argument must be specified at least once. Required.
Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes <String> Platform unit (PU) to filter out This argument must be specified at least once. Required.
Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list <String>
A read group filter expression in the form "attribute:value", where "attribute" is a two
character read group attribute such as "RG" or "PU". This argument must be specified at
least once. Required.
Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group <String> The name of the read group to keep Required.
Valid only if "ReadLengthReadFilter" is specified:
--max-read-length <Integer> Keep only reads with length at most equal to the specified value Required.
--min-read-length <Integer> Keep only reads with length at least equal to the specified value Default value: 1.
Valid only if "ReadNameReadFilter" is specified:
--read-name <String> Keep only reads with this read name This argument must be specified at least once.
Required.
Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only <Boolean>
Keep only reads on the reverse strand Required. Possible values: {true, false}
Valid only if "ReadTagValueFilter" is specified:
--read-filter-tag <String> Look for this tag in read Required.
--read-filter-tag-comp <Float>Compare value in tag to this value Default value: 0.0.
--read-filter-tag-op <Operator>
Compare value in tag to value with this operator. If T is the value in the tag, OP is the
operation provided, and V is the value in read-filter-tag, then the read will pass the
filter iff T OP V is true. Default value: EQUAL. Possible values: {LESS, LESS_OR_EQUAL,
GREATER, GREATER_OR_EQUAL, EQUAL, NOT_EQUAL}
Valid only if "SampleReadFilter" is specified:
--sample <String> The name of the sample(s) to keep, filtering out all others This argument must be
specified at least once. Required.
Valid only if "SoftClippedReadFilter" is specified:
--max-soft-clipped-leading-trailing-ratio <Double>
Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
in read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumSoftClippedRatio
--max-soft-clipped-ratio <Double>
Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumLeadingTrailingSoftClippedRatio
20:47:49.165 INFO FeatureManager - Using codec IntervalListCodec to read file file:///gatkCloneMountPoint/src/test/resources/picard_intervals.interval_list
20:47:49.167 INFO IntervalArgumentCollection - Processing 20 bp from intervals
20:47:49.168 INFO ProgressMeter - Starting traversal
20:47:49.168 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:49.168 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:49.168 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:49.182 INFO ProgressMeter - Starting traversal
20:47:49.182 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:49.182 INFO ProgressMeter - unmapped 0.0 0 NaN
20:47:49.182 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:49.201 INFO ProgressMeter - Starting traversal
20:47:49.201 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
20:47:49.256 INFO ProgressMeter - unmapped 0.0 0 0.0
20:47:49.257 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:49.272 INFO ProgressMeter - Starting traversal
20:47:49.272 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:49.288 INFO ProgressMeter - unmapped 0.0 0 0.0
20:47:49.289 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:49.304 INFO ProgressMeter - Starting traversal
20:47:49.304 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:47:49.331 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:49.331 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:49.331 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:49.331 INFO TestIntervalWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:49.331 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:49.331 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:47:49 PM GMT
20:47:49.331 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:49.331 INFO TestIntervalWalker - ------------------------------------------------------------
20:47:49.331 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:49.331 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:49.331 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:49.331 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:49.331 INFO TestIntervalWalker - Deflater: IntelDeflater
20:47:49.331 INFO TestIntervalWalker - Inflater: IntelInflater
20:47:49.331 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:47:49.331 INFO TestIntervalWalker - Requester pays: disabled
20:47:49.331 INFO TestIntervalWalker - Initializing engine
20:47:49.332 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:47:49 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912