19:48:11.045 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
19:48:11.073 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
19:48:11.153 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:48:11.157 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:48:11.159 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:48:11.163 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:48:11.165 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:48:11.169 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
19:48:11.191 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
19:48:11.198 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:48:11.203 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
19:48:11.207 INFO ProgressMeter - Starting traversal
19:48:11.207 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.207 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.207 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.240 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:48:11.240 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.240 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.241 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.241 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.241 INFO TestGATKToolWithFeatures - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.241 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:48:11.241 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:48:11.242 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.242 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.242 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.242 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.242 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
19:48:11.242 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
19:48:11.242 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
19:48:11.242 INFO TestGATKToolWithFeatures - Requester pays: disabled
19:48:11.242 INFO TestGATKToolWithFeatures - Initializing engine
19:48:11.243 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
19:48:11.244 INFO TestGATKToolWithFeatures - Done initializing engine
19:48:11.245 INFO ProgressMeter - Starting traversal
19:48:11.245 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.245 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.245 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.245 INFO TestGATKToolWithFeatures - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.262 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.263 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.263 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.263 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.263 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.263 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.263 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.263 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.263 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.263 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.264 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.264 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.264 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:48:11.264 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:48:11.264 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:48:11.264 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:48:11.264 INFO TestIntervalTransformingWalker - Initializing engine
19:48:11.265 INFO IntervalArgumentCollection - Processing 1 bp from intervals
19:48:11.266 INFO TestIntervalTransformingWalker - Done initializing engine
19:48:11.266 INFO ProgressMeter - Starting traversal
19:48:11.266 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.266 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.267 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.267 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.272 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.272 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.272 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.272 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.272 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.272 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.272 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.272 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.273 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.273 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.273 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.273 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.273 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:48:11.273 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:48:11.273 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:48:11.273 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:48:11.273 INFO TestIntervalTransformingWalker - Initializing engine
19:48:11.274 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
19:48:11.274 INFO TestIntervalTransformingWalker - Done initializing engine
19:48:11.274 INFO ProgressMeter - Starting traversal
19:48:11.274 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.275 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.275 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.275 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.280 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.280 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.280 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.280 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.280 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.280 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.280 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.280 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.281 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.281 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.281 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.281 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.281 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:48:11.281 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:48:11.281 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:48:11.281 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:48:11.281 INFO TestIntervalTransformingWalker - Initializing engine
19:48:11.282 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
19:48:11.282 INFO TestIntervalTransformingWalker - Done initializing engine
19:48:11.282 INFO ProgressMeter - Starting traversal
19:48:11.282 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.282 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.282 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.282 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.287 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.287 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.287 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.287 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.287 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.287 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.287 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.287 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.288 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.288 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.288 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.288 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.288 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:48:11.288 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:48:11.288 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:48:11.288 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:48:11.288 INFO TestIntervalTransformingWalker - Initializing engine
19:48:11.289 INFO TestIntervalTransformingWalker - Done initializing engine
19:48:11.289 INFO ProgressMeter - Starting traversal
19:48:11.289 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.289 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.289 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.289 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.294 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.294 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.294 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.294 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.294 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.294 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.294 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.295 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
19:48:11.295 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.295 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.295 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.295 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.295 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
19:48:11.295 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
19:48:11.295 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
19:48:11.295 INFO TestIntervalTransformingWalker - Requester pays: disabled
19:48:11.295 INFO TestIntervalTransformingWalker - Initializing engine
19:48:11.295 INFO TestIntervalTransformingWalker - Done initializing engine
19:48:11.295 INFO ProgressMeter - Starting traversal
19:48:11.295 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.295 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.296 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.296 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.301 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.301 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.301 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.301 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.301 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.301 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.301 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.301 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.301 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.301 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.301 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.302 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.302 INFO TestIntervalWalker - Deflater: IntelDeflater
19:48:11.302 INFO TestIntervalWalker - Inflater: IntelInflater
19:48:11.302 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:48:11.302 INFO TestIntervalWalker - Requester pays: disabled
19:48:11.302 INFO TestIntervalWalker - Initializing engine
19:48:11.302 INFO IntervalArgumentCollection - Processing 1 bp from intervals
19:48:11.302 INFO TestIntervalWalker - Done initializing engine
19:48:11.303 INFO ProgressMeter - Starting traversal
19:48:11.303 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.303 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.303 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.303 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.308 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.308 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.308 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.308 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.308 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.308 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.308 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.308 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.308 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.309 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.309 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.309 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.309 INFO TestIntervalWalker - Deflater: IntelDeflater
19:48:11.309 INFO TestIntervalWalker - Inflater: IntelInflater
19:48:11.309 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:48:11.309 INFO TestIntervalWalker - Requester pays: disabled
19:48:11.309 INFO TestIntervalWalker - Initializing engine
19:48:11.310 INFO TestIntervalWalker - Done initializing engine
19:48:11.310 INFO ProgressMeter - Starting traversal
19:48:11.310 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.310 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.310 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.310 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.314 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.315 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.315 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.315 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.315 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.315 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.315 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.315 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.315 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.315 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.315 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.315 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.315 INFO TestIntervalWalker - Deflater: IntelDeflater
19:48:11.315 INFO TestIntervalWalker - Inflater: IntelInflater
19:48:11.315 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:48:11.315 INFO TestIntervalWalker - Requester pays: disabled
19:48:11.315 INFO TestIntervalWalker - Initializing engine
19:48:11.316 INFO TestIntervalWalker - Done initializing engine
19:48:11.316 INFO ProgressMeter - Starting traversal
19:48:11.316 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.316 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.316 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.316 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:null
Optional Arguments:
--add-output-sam-program-record <Boolean>
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}
--add-output-vcf-command-line <Boolean>
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}
--annotation,-A <String> One or more specific annotations to add to variant calls This argument may be specified 0
or more times. Default value: null. Possible values: {AlleleFraction, AllelePseudoDepth,
AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
AS_StrandBiasMutectAnnotation, AS_StrandOddsRatio, AssemblyComplexity, BaseQuality,
BaseQualityHistogram, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest,
CountNs, Coverage, CycleSkipStatus, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet,
FisherStrand, FragmentDepthPerAlleleBySample, FragmentLength, GcContent,
GenotypeSummaries, HaplotypeFilteringAnnotation, HmerIndelLength, HmerIndelNuc,
HmerMotifs, InbreedingCoeff, IndelClassify, IndelLength, LikelihoodRankSumTest,
MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts,
OriginalAlignment, PossibleDeNovo, QualByDepth, RawGtCount, ReadPosition,
ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample,
StrandOddsRatio, TandemRepeat, TransmittedSingleton, UniqueAltReadCount, VariantType}
--annotation-group,-G <String>One or more groups of annotations to apply to variant calls This argument may be
specified 0 or more times. Default value: null. Possible values:
{AlleleSpecificAnnotation, AS_StandardAnnotation, GenotypeAnnotation, InfoFieldAnnotation,
JumboGenotypeAnnotation, JumboInfoAnnotation, ReducibleAnnotation, StandardAnnotation,
StandardFlowBasedAnnotation, StandardHCAnnotation, StandardMutectAnnotation,
VariantAnnotation}
--annotations-to-exclude,-AX <String>
One or more specific annotations to exclude from variant calls This argument may be
specified 0 or more times. Default value: null. Any value allowed
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--cloud-index-prefetch-buffer,-CIPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
cloudPrefetchBuffer if unset. Default value: -1.
--cloud-prefetch-buffer,-CPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
--create-output-bam-index,-OBI <Boolean>
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}
--create-output-bam-md5,-OBM <Boolean>
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}
--create-output-variant-index,-OVI <Boolean>
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}
--create-output-variant-md5,-OVM <Boolean>
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}
--disable-bam-index-caching,-DBIC <Boolean>
If true, don't cache bam indexes, this will reduce memory requirements but may harm
performance if many intervals are specified. Caching is automatically disabled if there
are no intervals specified. Default value: false. Possible values: {true, false}
--disable-read-filter,-DF <String>
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {WellformedReadFilter}
--disable-sequence-dictionary-validation <Boolean>
If specified, do not check the sequence dictionaries from our inputs for compatibility.
Use at your own risk! Default value: false. Possible values: {true, false}
--exclude-intervals,-XL <String>
One or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.
--flow-order-for-annotations <String>
flow order used for this annotations. [readGroup:]flowOrder This argument may be
specified 0 or more times. Default value: null.
--founder-id <String> Samples representing the population "founders" This argument may be specified 0 or more
times. Default value: null.
--gatk-config-file <String> A configuration file to use with the GATK. Default value: null.
--gcs-max-retries,-gcs-retries <Integer>
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.
--gcs-project-for-requester-pays <String>
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. User must have storage.buckets.get permission on the bucket being accessed.
Default value: .
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--input,-I <GATKPath> BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
Default value: null.
--interval-exclusion-padding,-ixp <Integer>
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
--interval-merging-rule,-imr <IntervalMergingRule>
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}
--interval-padding,-ip <Integer>
Amount of padding (in bp) to add to each interval you are including. Default value: 0.
--interval-set-rule,-isr <IntervalSetRule>
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}
--intervals,-L <String> One or more genomic intervals over which to operate This argument may be specified 0 or
more times. Default value: null.
--inverted-read-filter,-XRF <String>
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis
(after regular read filters). This argument may be specified 0 or more times. Default
value: null.
--lenient,-LE <Boolean> Lenient processing of VCF files Default value: false. Possible values: {true, false}
--max-variants-per-shard <Integer>
If non-zero, partitions VCF output into shards, each containing up to the given number of
records. Default value: 0.
--output,-out <File> Input variants Default value: null.
--pedigree,-ped <GATKPath> Pedigree file for determining the population "founders" Default value: null.
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--read-filter,-RF <String> Read filters to be applied before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {AlignmentAgreesWithHeaderReadFilter,
AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
ExcessiveEndClippedReadFilter, FirstOfPairReadFilter,
FlowBasedTPAttributeSymetricReadFilter, FlowBasedTPAttributeValidReadFilter,
FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter,
HmerQualitySymetricReadFilter, IntervalOverlapReadFilter,
JexlExpressionReadTagValueFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupHasFlowOrderReadFilter,
ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter,
ReadNameReadFilter, ReadStrandFilter, ReadTagValueFilter, SampleReadFilter,
SecondOfPairReadFilter, SeqIsStoredReadFilter, SoftClippedReadFilter,
ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedFlowBasedReadFilter,
WellformedReadFilter}
--read-index <GATKPath> Indices to use for the read inputs. If specified, an index must be provided for every read
input and in the same order as the read inputs. If this argument is not specified, the
path to the index for each input will be inferred automatically. This argument may be
specified 0 or more times. Default value: null.
--read-validation-stringency,-VS <ValidationStringency>
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default
stringency value SILENT can improve performance when processing a BAM file in which
variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default
value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
--reference,-R <GATKPath> Reference sequence Default value: null.
--seconds-between-progress-updates <Double>
Output traversal statistics every time this many seconds elapse Default value: 10.0.
--sequence-dictionary <GATKPath>
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.
--sites-only-vcf-output <Boolean>
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}
--tmp-dir <GATKPath> Temp directory to use. Default value: null.
--use-jdk-deflater,-jdk-deflater <Boolean>
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}
--use-jdk-inflater,-jdk-inflater <Boolean>
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}
--verbosity <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--disable-tool-default-annotations <Boolean>
Disable all tool default annotations Default value: false. Possible values: {true, false}
--disable-tool-default-read-filters <Boolean>
Disable all tool default read filters (WARNING: many tools will not function correctly
without their default read filters on) Default value: false. Possible values: {true,
false}
--enable-all-annotations <Boolean>
Use all possible annotations (not for the faint of heart) Default value: false. Possible
values: {true, false}
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
Conditional Arguments for annotation:
Valid only if "AllelePseudoDepth" is specified:
--dirichlet-keep-prior-in-count <Boolean>
By default we don't keep the prior use in the output counts ase it makes it easier to
interpretthis quantity as the number of supporting reads specially in low depth sites. We
this toggled the prior is included Default value: false. Possible values: {true, false}
--dirichlet-prior-pseudo-count <Double>
Pseudo-count used as prior for all alleles. The default is 1.0 resulting in a flat prior
Default value: 1.0.
--pseudo-count-weight-decay-rate <Double>
A what rate the weight of a read decreases base on its informativeness; e.g. 1.0 is linear
decay (default), 2.0 is for quadratic decay Default value: 1.0.
Valid only if "AssemblyComplexity" is specified:
--assembly-complexity-reference-mode <Boolean>
If enabled will treat the reference as the basis for assembly complexity as opposed to
estimated germline haplotypes Default value: false. Possible values: {true, false}
Valid only if "PossibleDeNovo" is specified:
--denovo-depth-threshold <Integer>
Minimum depth (DP) for all trio members to be considered for de novo calculation. Default
value: 0.
--denovo-parent-gq-threshold <Integer>
Minimum genotype quality for parents to be considered for de novo calculation (separate
from GQ thershold for full trio). Default value: 20.
Valid only if "RMSMappingQuality" is specified:
--allow-old-rms-mapping-quality-annotation-data <Boolean>
Override to allow old RMSMappingQuality annotated VCFs to function Default value: false.
Possible values: {true, false}
Conditional Arguments for readFilter:
Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases <Integer>Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
overrides threshold fraction. Default value: null. Cannot be used in conjunction with
argument(s) maxAmbiguousBaseFraction
--ambig-filter-frac <Double> Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjunction
with argument(s) maxAmbiguousBases
Valid only if "ExcessiveEndClippedReadFilter" is specified:
--max-clipped-bases <Integer> Maximum number of clipped bases on either end of a given read Default value: 1000.
Valid only if "FlowBasedTPAttributeValidReadFilter" is specified:
--read-filter-max-hmer <Integer>
maxHmer to use for testing in the filter Default value: 12.
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length <Integer>
Maximum length of fragment (insert size) Default value: 1000000.
--min-fragment-length <Integer>
Minimum length of fragment (insert size) Default value: 0.
Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals <String> One or more genomic intervals to keep This argument must be specified at least once.
Required.
Valid only if "JexlExpressionReadTagValueFilter" is specified:
--read-filter-expression <String>
One or more JEXL expressions used to filter This argument must be specified at least
once. Required.
Valid only if "LibraryReadFilter" is specified:
--library <String> Name of the library to keep This argument must be specified at least once. Required.
Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality <Integer>
Maximum mapping quality to keep (inclusive) Default value: null.
--minimum-mapping-quality <Integer>
Minimum mapping quality to keep (inclusive) Default value: 10.
Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length <Integer>
Minimum start location difference at which mapped mates are considered distant Default
value: 1000.
Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends <Boolean>
Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
block Default value: false. Possible values: {true, false}
--filter-too-short <Integer> Minimum number of aligned bases Default value: 30.
Valid only if "PlatformReadFilter" is specified:
--platform-filter-name <String>
Platform attribute (PL) to match This argument must be specified at least once. Required.
Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes <String> Platform unit (PU) to filter out This argument must be specified at least once. Required.
Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list <String>
A read group filter expression in the form "attribute:value", where "attribute" is a two
character read group attribute such as "RG" or "PU". This argument must be specified at
least once. Required.
Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group <String> The name of the read group to keep Required.
Valid only if "ReadLengthReadFilter" is specified:
--max-read-length <Integer> Keep only reads with length at most equal to the specified value Required.
--min-read-length <Integer> Keep only reads with length at least equal to the specified value Default value: 1.
Valid only if "ReadNameReadFilter" is specified:
--read-name <String> Keep only reads with this read name This argument must be specified at least once.
Required.
Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only <Boolean>
Keep only reads on the reverse strand Required. Possible values: {true, false}
Valid only if "ReadTagValueFilter" is specified:
--read-filter-tag <String> Look for this tag in read Required.
--read-filter-tag-comp <Float>Compare value in tag to this value Default value: 0.0.
--read-filter-tag-op <Operator>
Compare value in tag to value with this operator. If T is the value in the tag, OP is the
operation provided, and V is the value in read-filter-tag, then the read will pass the
filter iff T OP V is true. Default value: EQUAL. Possible values: {LESS, LESS_OR_EQUAL,
GREATER, GREATER_OR_EQUAL, EQUAL, NOT_EQUAL}
Valid only if "SampleReadFilter" is specified:
--sample <String> The name of the sample(s) to keep, filtering out all others This argument must be
specified at least once. Required.
Valid only if "SoftClippedReadFilter" is specified:
--max-soft-clipped-leading-trailing-ratio <Double>
Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
in read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumSoftClippedRatio
--max-soft-clipped-ratio <Double>
Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumLeadingTrailingSoftClippedRatio
19:48:11.361 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/picard_intervals.interval_list
19:48:11.363 INFO IntervalArgumentCollection - Processing 20 bp from intervals
19:48:11.363 INFO ProgressMeter - Starting traversal
19:48:11.364 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.364 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.364 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.375 INFO ProgressMeter - Starting traversal
19:48:11.375 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.375 INFO ProgressMeter - unmapped 0.0 0 NaN
19:48:11.375 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.386 INFO ProgressMeter - Starting traversal
19:48:11.386 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
19:48:11.440 INFO ProgressMeter - unmapped 0.0 0 0.0
19:48:11.440 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.446 INFO ProgressMeter - Starting traversal
19:48:11.446 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.461 INFO ProgressMeter - unmapped 0.0 0 0.0
19:48:11.461 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:48:11.468 INFO ProgressMeter - Starting traversal
19:48:11.468 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
19:48:11.484 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.484 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.484 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.484 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.484 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.485 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.485 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.485 INFO TestIntervalWalker - ------------------------------------------------------------
19:48:11.485 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.485 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.485 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.485 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.485 INFO TestIntervalWalker - Deflater: IntelDeflater
19:48:11.485 INFO TestIntervalWalker - Inflater: IntelInflater
19:48:11.485 INFO TestIntervalWalker - GCS max retries/reopens: 20
19:48:11.485 INFO TestIntervalWalker - Requester pays: disabled
19:48:11.485 INFO TestIntervalWalker - Initializing engine
19:48:11.486 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600