22:32:01.795 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
22:32:01.818 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
22:32:01.911 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:32:01.915 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:32:01.917 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:32:01.922 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:32:01.923 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:32:01.928 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
22:32:01.949 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
22:32:01.958 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:32:01.966 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
22:32:01.971 INFO ProgressMeter - Starting traversal
22:32:01.971 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:01.972 INFO ProgressMeter - unmapped 0.0 0 0.0
22:32:01.972 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.013 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:32:02.013 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.013 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.013 INFO TestGATKToolWithFeatures - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.014 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.014 INFO TestGATKToolWithFeatures - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.014 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:32:02.014 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:32:02.014 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.014 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.014 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.014 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.015 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
22:32:02.015 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
22:32:02.015 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
22:32:02.015 INFO TestGATKToolWithFeatures - Requester pays: disabled
22:32:02.015 INFO TestGATKToolWithFeatures - Initializing engine
22:32:02.016 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
22:32:02.018 INFO TestGATKToolWithFeatures - Done initializing engine
22:32:02.018 INFO ProgressMeter - Starting traversal
22:32:02.018 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.018 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.018 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.018 INFO TestGATKToolWithFeatures - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.038 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.038 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.038 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.038 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.038 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.038 INFO TestIntervalTransformingWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.038 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.038 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.039 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.039 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.039 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.039 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.039 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:32:02.039 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:32:02.039 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:32:02.039 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:32:02.039 INFO TestIntervalTransformingWalker - Initializing engine
22:32:02.040 INFO IntervalArgumentCollection - Processing 1 bp from intervals
22:32:02.042 INFO TestIntervalTransformingWalker - Done initializing engine
22:32:02.042 INFO ProgressMeter - Starting traversal
22:32:02.042 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.042 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.042 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.042 INFO TestIntervalTransformingWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.049 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.049 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.049 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.049 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.049 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.049 INFO TestIntervalTransformingWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.049 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.049 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.049 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.049 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.049 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.049 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.049 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:32:02.050 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:32:02.050 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:32:02.050 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:32:02.050 INFO TestIntervalTransformingWalker - Initializing engine
22:32:02.051 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
22:32:02.051 INFO TestIntervalTransformingWalker - Done initializing engine
22:32:02.051 INFO ProgressMeter - Starting traversal
22:32:02.051 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.051 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.051 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.051 INFO TestIntervalTransformingWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.057 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.057 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.057 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.057 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.057 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.057 INFO TestIntervalTransformingWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.057 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.057 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.058 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.058 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.058 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.058 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.058 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:32:02.058 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:32:02.058 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:32:02.058 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:32:02.058 INFO TestIntervalTransformingWalker - Initializing engine
22:32:02.059 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
22:32:02.059 INFO TestIntervalTransformingWalker - Done initializing engine
22:32:02.059 INFO ProgressMeter - Starting traversal
22:32:02.059 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.059 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.060 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.060 INFO TestIntervalTransformingWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.066 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.066 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.066 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.066 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.066 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.066 INFO TestIntervalTransformingWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.066 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.066 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.066 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.066 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.066 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.067 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.067 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:32:02.067 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:32:02.067 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:32:02.067 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:32:02.067 INFO TestIntervalTransformingWalker - Initializing engine
22:32:02.068 INFO TestIntervalTransformingWalker - Done initializing engine
22:32:02.068 INFO ProgressMeter - Starting traversal
22:32:02.068 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.068 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.068 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.068 INFO TestIntervalTransformingWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.074 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.074 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.074 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.075 INFO TestIntervalTransformingWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.075 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.075 INFO TestIntervalTransformingWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.075 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.075 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
22:32:02.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.075 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.075 INFO TestIntervalTransformingWalker - Deflater: IntelDeflater
22:32:02.075 INFO TestIntervalTransformingWalker - Inflater: IntelInflater
22:32:02.075 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
22:32:02.075 INFO TestIntervalTransformingWalker - Requester pays: disabled
22:32:02.076 INFO TestIntervalTransformingWalker - Initializing engine
22:32:02.076 INFO TestIntervalTransformingWalker - Done initializing engine
22:32:02.076 INFO ProgressMeter - Starting traversal
22:32:02.076 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.076 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.076 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.076 INFO TestIntervalTransformingWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.083 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.083 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.083 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.083 INFO TestIntervalWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.083 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.084 INFO TestIntervalWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.084 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.084 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.084 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.084 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.084 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.084 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.084 INFO TestIntervalWalker - Deflater: IntelDeflater
22:32:02.084 INFO TestIntervalWalker - Inflater: IntelInflater
22:32:02.084 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:32:02.084 INFO TestIntervalWalker - Requester pays: disabled
22:32:02.085 INFO TestIntervalWalker - Initializing engine
22:32:02.085 INFO IntervalArgumentCollection - Processing 1 bp from intervals
22:32:02.085 INFO TestIntervalWalker - Done initializing engine
22:32:02.086 INFO ProgressMeter - Starting traversal
22:32:02.086 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.086 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.086 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.086 INFO TestIntervalWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.094 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.094 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.094 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.094 INFO TestIntervalWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.094 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.094 INFO TestIntervalWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.095 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.095 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.095 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.095 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.095 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.095 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.095 INFO TestIntervalWalker - Deflater: IntelDeflater
22:32:02.095 INFO TestIntervalWalker - Inflater: IntelInflater
22:32:02.095 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:32:02.095 INFO TestIntervalWalker - Requester pays: disabled
22:32:02.095 INFO TestIntervalWalker - Initializing engine
22:32:02.096 INFO TestIntervalWalker - Done initializing engine
22:32:02.096 INFO ProgressMeter - Starting traversal
22:32:02.096 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.096 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.096 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.096 INFO TestIntervalWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.102 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.102 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.102 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.102 INFO TestIntervalWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.102 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.102 INFO TestIntervalWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.102 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.102 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.102 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.102 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.102 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.102 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.102 INFO TestIntervalWalker - Deflater: IntelDeflater
22:32:02.103 INFO TestIntervalWalker - Inflater: IntelInflater
22:32:02.103 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:32:02.103 INFO TestIntervalWalker - Requester pays: disabled
22:32:02.103 INFO TestIntervalWalker - Initializing engine
22:32:02.103 INFO TestIntervalWalker - Done initializing engine
22:32:02.103 INFO ProgressMeter - Starting traversal
22:32:02.103 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.103 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.103 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.103 INFO TestIntervalWalker - Shutting down engine
[March 28, 2025 at 10:32:02 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
22:32:02.154 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/picard_intervals.interval_list
22:32:02.157 INFO IntervalArgumentCollection - Processing 20 bp from intervals
22:32:02.157 INFO ProgressMeter - Starting traversal
22:32:02.157 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.157 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.158 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.163 INFO ProgressMeter - Starting traversal
22:32:02.163 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.163 INFO ProgressMeter - unmapped 0.0 0 NaN
22:32:02.163 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.181 INFO ProgressMeter - Starting traversal
22:32:02.181 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
22:32:02.243 INFO ProgressMeter - unmapped 0.0 0 0.0
22:32:02.243 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.252 INFO ProgressMeter - Starting traversal
22:32:02.252 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.274 INFO ProgressMeter - unmapped 0.0 0 0.0
22:32:02.274 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:32:02.282 INFO ProgressMeter - Starting traversal
22:32:02.282 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
22:32:02.301 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.301 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.301 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.301 INFO TestIntervalWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.301 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.301 INFO TestIntervalWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.301 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.301 INFO TestIntervalWalker - ------------------------------------------------------------
22:32:02.301 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.301 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.301 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.301 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.302 INFO TestIntervalWalker - Deflater: IntelDeflater
22:32:02.302 INFO TestIntervalWalker - Inflater: IntelInflater
22:32:02.302 INFO TestIntervalWalker - GCS max retries/reopens: 20
22:32:02.302 INFO TestIntervalWalker - Requester pays: disabled
22:32:02.302 INFO TestIntervalWalker - Initializing engine
22:32:02.302 INFO TestIntervalWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600