22:03:37.409 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
22:03:37.469 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
22:03:37.773 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:03:37.777 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:03:37.778 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:03:37.781 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:03:37.783 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:03:37.787 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:03:37.825 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
22:03:37.852 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:03:37.867 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
22:03:37.871 INFO ProgressMeter - Starting traversal
22:03:37.871 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:37.871 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:37.871 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:37.980 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:03:37.980 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:37.981 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:37.981 INFO TestGATKToolWithFeatures - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:37.981 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:37.981 INFO TestGATKToolWithFeatures - Start Date/Time: April 22, 2025 at 10:03:37 PM GMT
22:03:37.981 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:03:37.981 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:03:37.981 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:37.981 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:37.981 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:37.981 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:37.981 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
22:03:37.981 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
22:03:37.982 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
22:03:37.982 INFO TestGATKToolWithFeatures - Requester pays: disabled
22:03:37.982 INFO TestGATKToolWithFeatures - Initializing engine
22:03:37.983 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
22:03:37.985 INFO TestGATKToolWithFeatures - Done initializing engine
22:03:37.985 INFO ProgressMeter - Starting traversal
22:03:37.985 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:37.985 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:37.985 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:37.985 INFO TestGATKToolWithFeatures - Shutting down engine
[April 22, 2025 at 10:03:37 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.037 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.037 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.037 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.037 INFO TestIntervalTransformingWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.037 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.038 INFO TestIntervalTransformingWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.038 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.038 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.038 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.038 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.038 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.038 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.038 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:03:38.038 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:03:38.038 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:03:38.038 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:03:38.038 INFO TestIntervalTransformingWalker - Initializing engine
22:03:38.039 INFO IntervalArgumentCollection - Processing 1 bp from intervals
22:03:38.040 INFO TestIntervalTransformingWalker - Done initializing engine
22:03:38.040 INFO ProgressMeter - Starting traversal
22:03:38.040 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.041 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.041 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.041 INFO TestIntervalTransformingWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.056 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.056 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.056 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.056 INFO TestIntervalTransformingWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.056 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.056 INFO TestIntervalTransformingWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.056 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.056 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.056 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.056 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.056 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.056 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.057 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:03:38.057 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:03:38.057 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:03:38.057 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:03:38.057 INFO TestIntervalTransformingWalker - Initializing engine
22:03:38.058 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
22:03:38.058 INFO TestIntervalTransformingWalker - Done initializing engine
22:03:38.058 INFO ProgressMeter - Starting traversal
22:03:38.058 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.058 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.058 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.058 INFO TestIntervalTransformingWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.074 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.075 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.075 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.075 INFO TestIntervalTransformingWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.075 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.075 INFO TestIntervalTransformingWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.075 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.075 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.075 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:03:38.075 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:03:38.075 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:03:38.075 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:03:38.075 INFO TestIntervalTransformingWalker - Initializing engine
22:03:38.076 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
22:03:38.077 INFO TestIntervalTransformingWalker - Done initializing engine
22:03:38.077 INFO ProgressMeter - Starting traversal
22:03:38.077 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.077 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.077 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.077 INFO TestIntervalTransformingWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.091 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.092 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.092 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.092 INFO TestIntervalTransformingWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.092 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.092 INFO TestIntervalTransformingWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.092 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.092 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.092 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.092 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.092 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.092 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.092 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:03:38.092 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:03:38.092 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:03:38.093 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:03:38.093 INFO TestIntervalTransformingWalker - Initializing engine
22:03:38.093 INFO TestIntervalTransformingWalker - Done initializing engine
22:03:38.093 INFO ProgressMeter - Starting traversal
22:03:38.093 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.093 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.094 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.094 INFO TestIntervalTransformingWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.108 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.108 INFO TestIntervalTransformingWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.108 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.108 INFO TestIntervalTransformingWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.109 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.109 INFO TestIntervalTransformingWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.109 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.109 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:03:38.109 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.109 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.109 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.109 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.109 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:03:38.109 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:03:38.109 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:03:38.109 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:03:38.109 INFO TestIntervalTransformingWalker - Initializing engine
22:03:38.110 INFO TestIntervalTransformingWalker - Done initializing engine
22:03:38.110 INFO ProgressMeter - Starting traversal
22:03:38.110 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.110 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.110 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.110 INFO TestIntervalTransformingWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.124 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.124 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.124 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.124 INFO TestIntervalWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.124 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.124 INFO TestIntervalWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.124 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.124 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.125 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.125 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.125 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.125 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.125 INFO TestIntervalWalker - Deflater: IntelDeflater
22:03:38.125 INFO TestIntervalWalker - Inflater: IntelInflater
22:03:38.125 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:03:38.125 INFO TestIntervalWalker - Requester pays: disabled
22:03:38.125 INFO TestIntervalWalker - Initializing engine
22:03:38.126 INFO IntervalArgumentCollection - Processing 1 bp from intervals
22:03:38.126 INFO TestIntervalWalker - Done initializing engine
22:03:38.126 INFO ProgressMeter - Starting traversal
22:03:38.126 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.126 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.126 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.126 INFO TestIntervalWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.140 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.140 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.140 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.140 INFO TestIntervalWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.140 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.141 INFO TestIntervalWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.141 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.141 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.141 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.141 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.141 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.141 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.141 INFO TestIntervalWalker - Deflater: IntelDeflater
22:03:38.141 INFO TestIntervalWalker - Inflater: IntelInflater
22:03:38.141 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:03:38.141 INFO TestIntervalWalker - Requester pays: disabled
22:03:38.141 INFO TestIntervalWalker - Initializing engine
22:03:38.142 INFO TestIntervalWalker - Done initializing engine
22:03:38.142 INFO ProgressMeter - Starting traversal
22:03:38.142 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.142 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.142 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.142 INFO TestIntervalWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:38.157 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.157 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.157 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.158 INFO TestIntervalWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.158 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.158 INFO TestIntervalWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.158 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.158 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.158 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.158 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.158 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.158 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.158 INFO TestIntervalWalker - Deflater: IntelDeflater
22:03:38.158 INFO TestIntervalWalker - Inflater: IntelInflater
22:03:38.158 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:03:38.158 INFO TestIntervalWalker - Requester pays: disabled
22:03:38.158 INFO TestIntervalWalker - Initializing engine
22:03:38.158 INFO TestIntervalWalker - Done initializing engine
22:03:38.158 INFO ProgressMeter - Starting traversal
22:03:38.158 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.159 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.159 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.159 INFO TestIntervalWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:4.6.2.0-2-gfa08e16-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
22:03:38.346 INFO FeatureManager - Using codec IntervalListCodec to read file file:///gatkCloneMountPoint/src/test/resources/picard_intervals.interval_list
22:03:38.348 INFO IntervalArgumentCollection - Processing 20 bp from intervals
22:03:38.349 INFO ProgressMeter - Starting traversal
22:03:38.349 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.349 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.349 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.362 INFO ProgressMeter - Starting traversal
22:03:38.362 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.363 INFO ProgressMeter - unmapped 0.0 0 NaN
22:03:38.363 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.381 INFO ProgressMeter - Starting traversal
22:03:38.381 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
22:03:38.436 INFO ProgressMeter - unmapped 0.0 0 0.0
22:03:38.436 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.452 INFO ProgressMeter - Starting traversal
22:03:38.452 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.468 INFO ProgressMeter - unmapped 0.0 0 0.0
22:03:38.468 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:38.482 INFO ProgressMeter - Starting traversal
22:03:38.482 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:03:38.508 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.508 INFO TestIntervalWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:38.508 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:38.508 INFO TestIntervalWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:38.508 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:38.508 INFO TestIntervalWalker - Start Date/Time: April 22, 2025 at 10:03:38 PM GMT
22:03:38.508 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.508 INFO TestIntervalWalker - ------------------------------------------------------------
22:03:38.508 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:38.509 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:38.509 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:38.509 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:38.509 INFO TestIntervalWalker - Deflater: IntelDeflater
22:03:38.509 INFO TestIntervalWalker - Inflater: IntelInflater
22:03:38.509 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:03:38.509 INFO TestIntervalWalker - Requester pays: disabled
22:03:38.509 INFO TestIntervalWalker - Initializing engine
22:03:38.509 INFO TestIntervalWalker - Shutting down engine
[April 22, 2025 at 10:03:38 PM GMT] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968