20:25:20.255 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
20:25:20.317 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
20:25:20.670 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:25:20.674 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:25:20.676 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:25:20.679 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:25:20.680 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:25:20.684 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:25:20.717 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
20:25:20.745 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:25:20.769 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
20:25:20.773 INFO ProgressMeter - Starting traversal
20:25:20.773 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:20.773 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:20.773 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:20.892 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:25:20.893 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:20.893 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:20.893 INFO TestGATKToolWithFeatures - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:20.893 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:20.893 INFO TestGATKToolWithFeatures - Start Date/Time: February 10, 2025 at 8:25:20 PM GMT
20:25:20.893 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:25:20.893 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:25:20.893 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:20.893 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:20.893 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:20.894 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:20.894 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:25:20.894 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:25:20.894 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:25:20.894 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:25:20.894 INFO TestGATKToolWithFeatures - Initializing engine
20:25:20.895 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
20:25:20.897 INFO TestGATKToolWithFeatures - Done initializing engine
20:25:20.897 INFO ProgressMeter - Starting traversal
20:25:20.897 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:20.897 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:20.897 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:20.897 INFO TestGATKToolWithFeatures - Shutting down engine
[February 10, 2025 at 8:25:20 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:20.945 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.945 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:20.945 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:20.946 INFO TestIntervalTransformingWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:20.946 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:20.946 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:25:20 PM GMT
20:25:20.946 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.946 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.946 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:20.946 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:20.946 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:20.946 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:20.946 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:25:20.946 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:25:20.946 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:25:20.946 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:25:20.946 INFO TestIntervalTransformingWalker - Initializing engine
20:25:20.947 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:25:20.949 INFO TestIntervalTransformingWalker - Done initializing engine
20:25:20.949 INFO ProgressMeter - Starting traversal
20:25:20.949 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:20.949 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:20.949 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:20.949 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:25:20 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:20.968 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.968 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:20.968 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:20.968 INFO TestIntervalTransformingWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:20.968 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:20.968 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:25:20 PM GMT
20:25:20.968 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.968 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.968 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:20.968 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:20.968 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:20.968 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:20.968 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:25:20.968 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:25:20.969 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:25:20.969 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:25:20.969 INFO TestIntervalTransformingWalker - Initializing engine
20:25:20.969 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
20:25:20.970 INFO TestIntervalTransformingWalker - Done initializing engine
20:25:20.970 INFO ProgressMeter - Starting traversal
20:25:20.970 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:20.970 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:20.970 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:20.970 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:25:20 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:20.986 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.986 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:20.986 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:20.986 INFO TestIntervalTransformingWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:20.986 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:20.986 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:25:20 PM GMT
20:25:20.986 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.986 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:20.986 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:20.986 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:20.986 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:20.986 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:20.986 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:25:20.986 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:25:20.987 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:25:20.987 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:25:20.987 INFO TestIntervalTransformingWalker - Initializing engine
20:25:20.987 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
20:25:20.988 INFO TestIntervalTransformingWalker - Done initializing engine
20:25:20.988 INFO ProgressMeter - Starting traversal
20:25:20.988 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:20.988 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:20.988 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:20.988 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:25:20 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.002 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:21.003 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.003 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.003 INFO TestIntervalTransformingWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.003 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.003 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.003 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:21.003 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:21.003 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.003 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.003 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.003 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.003 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:25:21.003 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:25:21.003 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:25:21.003 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:25:21.003 INFO TestIntervalTransformingWalker - Initializing engine
20:25:21.004 INFO TestIntervalTransformingWalker - Done initializing engine
20:25:21.004 INFO ProgressMeter - Starting traversal
20:25:21.004 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.004 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:21.004 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.004 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.019 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:21.019 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.019 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.019 INFO TestIntervalTransformingWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.019 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.019 INFO TestIntervalTransformingWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.020 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:21.020 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:25:21.020 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.020 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.020 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.020 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.020 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:25:21.020 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:25:21.020 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:25:21.020 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:25:21.020 INFO TestIntervalTransformingWalker - Initializing engine
20:25:21.020 INFO TestIntervalTransformingWalker - Done initializing engine
20:25:21.020 INFO ProgressMeter - Starting traversal
20:25:21.020 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.020 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:21.020 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.021 INFO TestIntervalTransformingWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.036 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.036 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.036 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.036 INFO TestIntervalWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.036 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.036 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.036 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.036 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.036 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.036 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.036 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.036 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.036 INFO TestIntervalWalker - Deflater: IntelDeflater
20:25:21.036 INFO TestIntervalWalker - Inflater: IntelInflater
20:25:21.036 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:25:21.036 INFO TestIntervalWalker - Requester pays: disabled
20:25:21.036 INFO TestIntervalWalker - Initializing engine
20:25:21.037 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:25:21.037 INFO TestIntervalWalker - Done initializing engine
20:25:21.037 INFO ProgressMeter - Starting traversal
20:25:21.037 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.037 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:21.037 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.037 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.052 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.052 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.052 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.052 INFO TestIntervalWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.052 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.053 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.053 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.053 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.053 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.053 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.053 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.053 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.053 INFO TestIntervalWalker - Deflater: IntelDeflater
20:25:21.053 INFO TestIntervalWalker - Inflater: IntelInflater
20:25:21.053 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:25:21.053 INFO TestIntervalWalker - Requester pays: disabled
20:25:21.053 INFO TestIntervalWalker - Initializing engine
20:25:21.054 INFO TestIntervalWalker - Done initializing engine
20:25:21.054 INFO ProgressMeter - Starting traversal
20:25:21.054 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.054 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:21.054 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.054 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.070 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.070 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.070 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.070 INFO TestIntervalWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.070 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.070 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.070 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.070 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.070 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.070 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.070 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.070 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.070 INFO TestIntervalWalker - Deflater: IntelDeflater
20:25:21.070 INFO TestIntervalWalker - Inflater: IntelInflater
20:25:21.070 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:25:21.070 INFO TestIntervalWalker - Requester pays: disabled
20:25:21.071 INFO TestIntervalWalker - Initializing engine
20:25:21.071 INFO TestIntervalWalker - Done initializing engine
20:25:21.071 INFO ProgressMeter - Starting traversal
20:25:21.071 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.071 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:21.071 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.071 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:4.6.1.0-11-gb2a05c7-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
20:25:21.266 INFO FeatureManager - Using codec IntervalListCodec to read file file:///gatkCloneMountPoint/src/test/resources/picard_intervals.interval_list
20:25:21.268 INFO IntervalArgumentCollection - Processing 20 bp from intervals
20:25:21.268 INFO ProgressMeter - Starting traversal
20:25:21.268 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.268 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:21.268 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.282 INFO ProgressMeter - Starting traversal
20:25:21.282 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.282 INFO ProgressMeter - unmapped 0.0 0 NaN
20:25:21.283 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.301 INFO ProgressMeter - Starting traversal
20:25:21.301 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
20:25:21.354 INFO ProgressMeter - unmapped 0.0 0 0.0
20:25:21.354 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.370 INFO ProgressMeter - Starting traversal
20:25:21.370 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.385 INFO ProgressMeter - unmapped 0.0 0 0.0
20:25:21.385 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:21.400 INFO ProgressMeter - Starting traversal
20:25:21.400 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:25:21.426 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.426 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.426 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.426 INFO TestIntervalWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.427 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.427 INFO TestIntervalWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.427 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.427 INFO TestIntervalWalker - ------------------------------------------------------------
20:25:21.427 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.427 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.427 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.427 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.427 INFO TestIntervalWalker - Deflater: IntelDeflater
20:25:21.427 INFO TestIntervalWalker - Inflater: IntelInflater
20:25:21.427 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:25:21.427 INFO TestIntervalWalker - Requester pays: disabled
20:25:21.427 INFO TestIntervalWalker - Initializing engine
20:25:21.427 INFO TestIntervalWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408