20:33:07.045 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
20:33:07.068 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
20:33:07.160 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:33:07.163 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:33:07.164 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:33:07.167 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:33:07.169 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:33:07.172 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
20:33:07.199 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
20:33:07.208 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:33:07.214 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
20:33:07.217 INFO ProgressMeter - Starting traversal
20:33:07.218 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.218 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.218 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.249 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:33:07.249 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.249 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.250 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.250 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.250 INFO TestGATKToolWithFeatures - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.250 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:33:07.250 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:33:07.250 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.250 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.250 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.250 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.251 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:33:07.251 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:33:07.251 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:33:07.251 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:33:07.251 INFO TestGATKToolWithFeatures - Initializing engine
20:33:07.252 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
20:33:07.253 INFO TestGATKToolWithFeatures - Done initializing engine
20:33:07.253 INFO ProgressMeter - Starting traversal
20:33:07.253 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.253 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.253 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.253 INFO TestGATKToolWithFeatures - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.271 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.271 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.271 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.271 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.271 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.271 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.271 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.271 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.272 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.272 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.272 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.272 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.272 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:33:07.272 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:33:07.272 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:33:07.272 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:33:07.272 INFO TestIntervalTransformingWalker - Initializing engine
20:33:07.273 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:33:07.274 INFO TestIntervalTransformingWalker - Done initializing engine
20:33:07.274 INFO ProgressMeter - Starting traversal
20:33:07.275 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.275 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.275 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.275 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.282 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.282 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.282 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.282 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.282 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.282 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.282 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.282 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.282 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.282 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.282 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.282 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.283 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:33:07.283 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:33:07.283 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:33:07.283 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:33:07.283 INFO TestIntervalTransformingWalker - Initializing engine
20:33:07.284 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
20:33:07.284 INFO TestIntervalTransformingWalker - Done initializing engine
20:33:07.284 INFO ProgressMeter - Starting traversal
20:33:07.284 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.284 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.284 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.284 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.290 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.290 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.290 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.290 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.290 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.290 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.291 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.291 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.291 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.291 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.291 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.291 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.291 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:33:07.291 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:33:07.291 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:33:07.291 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:33:07.291 INFO TestIntervalTransformingWalker - Initializing engine
20:33:07.292 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
20:33:07.292 INFO TestIntervalTransformingWalker - Done initializing engine
20:33:07.292 INFO ProgressMeter - Starting traversal
20:33:07.292 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.292 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.292 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.292 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.298 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.298 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.298 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.298 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.299 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.299 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.299 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.299 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.299 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.299 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.299 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.299 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.299 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:33:07.299 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:33:07.299 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:33:07.299 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:33:07.299 INFO TestIntervalTransformingWalker - Initializing engine
20:33:07.300 INFO TestIntervalTransformingWalker - Done initializing engine
20:33:07.300 INFO ProgressMeter - Starting traversal
20:33:07.300 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.300 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.300 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.300 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.306 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.306 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.306 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.306 INFO TestIntervalTransformingWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.306 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.306 INFO TestIntervalTransformingWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.306 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.306 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
20:33:07.306 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.306 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.306 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.306 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.306 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
20:33:07.306 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
20:33:07.307 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
20:33:07.307 INFO TestIntervalTransformingWalker - Requester pays: disabled
20:33:07.307 INFO TestIntervalTransformingWalker - Initializing engine
20:33:07.307 INFO TestIntervalTransformingWalker - Done initializing engine
20:33:07.307 INFO ProgressMeter - Starting traversal
20:33:07.307 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.307 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.307 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.307 INFO TestIntervalTransformingWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.312 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.312 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.312 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.312 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.312 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.312 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.312 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.312 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.313 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.313 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.313 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.313 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.313 INFO TestIntervalWalker - Deflater: IntelDeflater
20:33:07.313 INFO TestIntervalWalker - Inflater: IntelInflater
20:33:07.313 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:33:07.313 INFO TestIntervalWalker - Requester pays: disabled
20:33:07.313 INFO TestIntervalWalker - Initializing engine
20:33:07.314 INFO IntervalArgumentCollection - Processing 1 bp from intervals
20:33:07.314 INFO TestIntervalWalker - Done initializing engine
20:33:07.314 INFO ProgressMeter - Starting traversal
20:33:07.314 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.314 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.314 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.314 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.318 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.318 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.318 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.318 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.319 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.319 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.319 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.319 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.319 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.319 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.319 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.319 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.319 INFO TestIntervalWalker - Deflater: IntelDeflater
20:33:07.319 INFO TestIntervalWalker - Inflater: IntelInflater
20:33:07.319 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:33:07.319 INFO TestIntervalWalker - Requester pays: disabled
20:33:07.319 INFO TestIntervalWalker - Initializing engine
20:33:07.320 INFO TestIntervalWalker - Done initializing engine
20:33:07.320 INFO ProgressMeter - Starting traversal
20:33:07.320 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.320 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.320 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.320 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.325 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.325 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.325 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.325 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.325 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.325 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.325 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.325 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.325 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.325 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.325 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.325 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.325 INFO TestIntervalWalker - Deflater: IntelDeflater
20:33:07.326 INFO TestIntervalWalker - Inflater: IntelInflater
20:33:07.326 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:33:07.326 INFO TestIntervalWalker - Requester pays: disabled
20:33:07.326 INFO TestIntervalWalker - Initializing engine
20:33:07.326 INFO TestIntervalWalker - Done initializing engine
20:33:07.326 INFO ProgressMeter - Starting traversal
20:33:07.326 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.326 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.326 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.326 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:33:07 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
20:33:07.369 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/picard_intervals.interval_list
20:33:07.371 INFO IntervalArgumentCollection - Processing 20 bp from intervals
20:33:07.371 INFO ProgressMeter - Starting traversal
20:33:07.371 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.371 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.372 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.377 INFO ProgressMeter - Starting traversal
20:33:07.377 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.377 INFO ProgressMeter - unmapped 0.0 0 NaN
20:33:07.377 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.386 INFO ProgressMeter - Starting traversal
20:33:07.386 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
20:33:07.446 INFO ProgressMeter - unmapped 0.0 0 0.0
20:33:07.446 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.452 INFO ProgressMeter - Starting traversal
20:33:07.452 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.467 INFO ProgressMeter - unmapped 0.0 0 0.0
20:33:07.467 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:33:07.473 INFO ProgressMeter - Starting traversal
20:33:07.473 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
20:33:07.492 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.493 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.493 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.493 INFO TestIntervalWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.493 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.493 INFO TestIntervalWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.493 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.493 INFO TestIntervalWalker - ------------------------------------------------------------
20:33:07.493 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.493 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.493 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.493 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.493 INFO TestIntervalWalker - Deflater: IntelDeflater
20:33:07.493 INFO TestIntervalWalker - Inflater: IntelInflater
20:33:07.493 INFO TestIntervalWalker - GCS max retries/reopens: 20
20:33:07.493 INFO TestIntervalWalker - Requester pays: disabled
20:33:07.494 INFO TestIntervalWalker - Initializing engine
20:33:07.494 INFO TestIntervalWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600