Class org.broadinstitute.hellbender.engine.GATKToolUnitTest

81

tests

0

failures

0

ignored

0.513s

duration

100%

successful

Tests

Test Duration Result
TestGATKToolWithSequenceDictionaryException[0](/home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.dict, --input, /home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, null, null) 0.011s passed
TestGATKToolWithSequenceDictionaryException[1](/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict, --input, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, --reference, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.033s passed
TestGATKToolWithSequenceDictionaryException[2](/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict, --reference, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, null, null) 0.005s passed
TestGATKToolWithSequenceDictionaryException[3](/home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.dict, --reference, /home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19_chr1_1M.fasta, null, null) 0.005s passed
TestGATKToolWithSequenceDictionaryOk[0](/home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.dict, --input, /home/runner/work/gatk/gatk/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null, null) 0.006s passed
TestGATKToolWithSequenceDictionaryOk[1](/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict, --input, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, --reference, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.004s passed
TestGATKToolWithSequenceDictionaryOk[2](/home/runner/work/gatk/gatk/src/test/resources/hg19mini.dict, --reference, /home/runner/work/gatk/gatk/src/test/resources/hg19micro.fasta, null, null) 0.005s passed
TestGATKToolWithSequenceDictionaryOk[3](/home/runner/work/gatk/gatk/src/test/resources/hg19micro.dict, --reference, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, null, null) 0.004s passed
TestGATKToolWithSequenceDictionaryOk[4](/home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.dict, --reference, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, null, null) 0.003s passed
testAllowLexicographicallySortedVariantHeader 0.006s passed
testBestSequenceDictionary_fromNothing 0.003s passed
testBestSequenceDictionary_fromReads 0.005s passed
testBestSequenceDictionary_fromReadsAndReference 0.007s passed
testBestSequenceDictionary_fromVariants 0.008s passed
testClearDefaultAnnotations 0.006s passed
testClearDefaultAnnotationsGroups 0.006s passed
testCreateVCFWriterDefaults[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, true) 0.009s passed
testCreateVCFWriterDefaults[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, false, true) 0.007s passed
testCreateVCFWriterDefaults[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, false) 0.006s passed
testCreateVCFWriterDefaults[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, true, true) 0.007s passed
testCreateVCFWriterDefaults[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, false, true) 0.006s passed
testCreateVCFWriterDefaults[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, true, false) 0.007s passed
testCreateVCFWriterDefaults[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.bgz, .tbi, true, true) 0.007s passed
testCreateVCFWriterDefaults[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.gz, .tbi, false, true) 0.006s passed
testCreateVCFWriterDefaults[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.bgz, .tbi, true, false) 0.005s passed
testCreateVCFWriterLenientFalse[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, true) 0.006s passed
testCreateVCFWriterLenientFalse[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, false, true) 0.001s passed
testCreateVCFWriterLenientFalse[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, false) 0.002s passed
testCreateVCFWriterLenientTrue[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, true) 0.002s passed
testCreateVCFWriterLenientTrue[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, false, true) 0.002s passed
testCreateVCFWriterLenientTrue[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, false) 0.001s passed
testCreateVCFWriterWithNoSequenceDictionary[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, true) 0.001s passed
testCreateVCFWriterWithNoSequenceDictionary[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, false, true) 0.002s passed
testCreateVCFWriterWithNoSequenceDictionary[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, false) 0.001s passed
testCreateVCFWriterWithNoSequenceDictionary[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, true, true) 0.002s passed
testCreateVCFWriterWithNoSequenceDictionary[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, false, true) 0.001s passed
testCreateVCFWriterWithNoSequenceDictionary[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, true, false) 0.002s passed
testCreateVCFWriterWithNoSequenceDictionary[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.bgz, .tbi, true, true) 0.001s passed
testCreateVCFWriterWithNoSequenceDictionary[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.gz, .tbi, false, true) 0.002s passed
testCreateVCFWriterWithNoSequenceDictionary[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.bgz, .tbi, true, false) 0.002s passed
testCreateVCFWriterWithOptions[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, true) 0.001s passed
testCreateVCFWriterWithOptions[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, false, true) 0.001s passed
testCreateVCFWriterWithOptions[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf, .idx, true, false) 0.001s passed
testCreateVCFWriterWithOptions[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, true, true) 0.003s passed
testCreateVCFWriterWithOptions[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, false, true) 0.002s passed
testCreateVCFWriterWithOptions[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .bcf, .idx, true, false) 0.002s passed
testCreateVCFWriterWithOptions[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.bgz, .tbi, true, true) 0.003s passed
testCreateVCFWriterWithOptions[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.gz, .tbi, false, true) 0.002s passed
testCreateVCFWriterWithOptions[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/example_variants.vcf, .vcf.bgz, .tbi, true, false) 0.002s passed
testDisallowLexicographicallySortedVariantHeader_ifClashWithReference 0.009s passed
testExcludeAnnotation 0.008s passed
testFeaturesHeader 0.009s passed
testGetAllAnnotations 0.006s passed
testGetBestAvailableSequenceDictionaryWithMasterDictionary[0](/home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.dict, --input, /home/runner/work/gatk/gatk/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null, null, SAMSequenceDictionary:( sequences:1 length:1000000 md5:d022d5a669fc4f1db20e414b5702eee4)) 0.007s passed
testGetBestAvailableSequenceDictionaryWithMasterDictionary[1](/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict, --input, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, --reference, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c)) 0.004s passed
testGetBestAvailableSequenceDictionaryWithMasterDictionary[2](/home/runner/work/gatk/gatk/src/test/resources/hg19mini.dict, --reference, /home/runner/work/gatk/gatk/src/test/resources/hg19micro.fasta, null, null, SAMSequenceDictionary:( sequences:4 length:64000 md5:5508371427589f82040a586d73c0aa6f)) 0.004s passed
testGetBestAvailableSequenceDictionaryWithMasterDictionary[3](/home/runner/work/gatk/gatk/src/test/resources/hg19micro.dict, --reference, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta, null, null, SAMSequenceDictionary:( sequences:2 length:32000 md5:be21a40d2d1a17c1f5b1f995d982e489)) 0.003s passed
testGetDefaultToolVCFHeaderLines 0.011s passed
testGetMasterSequenceDictionary[0](null, /home/runner/work/gatk/gatk/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.005s passed
testGetMasterSequenceDictionary[1](/home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.dict, /home/runner/work/gatk/gatk/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, SAMSequenceDictionary:( sequences:1 length:1000000 md5:d022d5a669fc4f1db20e414b5702eee4)) 0.004s passed
testGetTransformedTraversalIntervals[0]([1:21-21], 1, [1], [21], [21], /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta) 0.009s passed
testGetTransformedTraversalIntervals[1]([1:21-21, 1:23-23, 1:200-300, 1:10000-16000], 1, [1], [21], [16000], /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta) 0.009s passed
testGetTransformedTraversalIntervals[2]([1:21-21, 2:42-45, 2:10000-12345, 3:33-333], 3, [1, 2, 3], [21, 42, 33], [21, 12345, 333], /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta) 0.009s passed
testGetTransformedTraversalIntervals[3](null, 4, [1, 2, 3, 4], [1, 1, 1, 1], [16000, 16000, 16000, 16000], /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta) 0.008s passed
testGetTransformedTraversalIntervals[4](null, null, null, null, null, null) 0.006s passed
testGetTraversalIntervals[0](1:21-21, 1, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta) 0.006s passed
testGetTraversalIntervals[1](null, 4, /home/runner/work/gatk/gatk/src/test/resources/hg19mini.fasta) 0.005s passed
testGetTraversalIntervals[2](null, null, null) 0.005s passed
testHelpWithAllPluginDescriptors 0.010s passed
testIncludeAnnotation 0.005s passed
testIncludeAnnotationGroups 0.006s passed
testMakeDefaultAnnotationGroups 0.005s passed
testMakeDefaultAnnotations 0.004s passed
testMakeEmptyAnnotations 0.003s passed
testNonExistentReferenceFile 0.001s passed
testPicardIntervalList 0.009s passed
testReadsHeader 0.005s passed
testReadsValidationStringencyLenient[0](/home/runner/work/gatk/gatk/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, 493) 0.069s passed
testReadsValidationStringencySilent[0](/home/runner/work/gatk/gatk/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, 493) 0.021s passed
testReadsValidationStringencyStrict[0](/home/runner/work/gatk/gatk/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, 493) 0.019s passed
testSequenceDictionaryRequiredForIntervalQuery 0.007s passed

Standard error

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