Class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.variantutils > ReblockGVCFIntegrationTest

tests

failures

ignored

12.458s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testASAnnotationsAndSubsetting	3.460s	passed
testAddedHcAsAnnotations	0.118s	passed
testAggressiveQualFiltering	0.075s	passed
testContiguityWithSpanningDels	0.379s	passed
testDragenGvcfs	0.189s	passed
testFilters	0.221s	passed
testFirstPositionOnContigNotDropped	0.128s	passed
testGVCFReblockingIsContiguous	4.655s	passed
testHomRefCalls	0.197s	passed
testLeftContigBoundary	0.159s	passed
testMQHeadersAreUpdated	0.215s	passed
testMixedSamples	0.141s	passed
testMovingFilters	0.190s	passed
testMultipleInputs	0.281s	passed
testNewCompressionScheme	0.081s	passed
testNoCallGenotypes	0.130s	passed
testNoCallWhenGQ0InNonRefAllele	0.124s	passed
testNonGVCFInput	0.074s	passed
testNonRefADCorrection	0.074s	passed
testOneSampleAsForGnomAD	0.071s	passed
testOverlappingDeletions	0.201s	passed
testPosteriorDisagreementNeedingSubset	0.127s	passed
testRawMQInput	0.108s	passed
testReReblocking	0.191s	passed
testRemovingAnnotationFromEmptyAttributes	0.134s	passed
testRemovingFormatAnnotations	0.174s	passed
testSpanDelRegression	0.078s	passed
testTreeScoreThreshold	0.073s	passed
testTreeScoreWithNoAnnotation	0.072s	passed
testWithExactComparison[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/gvcfForReblocking.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf, -L chr20:69771 -rgq-threshold 19, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)	0.073s	passed
testWithExactComparison[1](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWgsInput.g.vcf , src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWgsOutput.g.vcf, -do-qual-approx --floor-blocks -GQB 20 -GQB 30 -GQB 40 , /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.133s	passed
testWithExactComparison[2](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWesInput.g.vcf , src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWesOutput.g.vcf, -do-qual-approx --floor-blocks -GQB 20 -GQB 30 -GQB 40 , /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.132s	passed

Standard output

--------------------------------------------------------------------------------
[14:32:21] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[14:32:21] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[14:32:24] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[14:32:31] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[14:32:31] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[14:32:31] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[14:32:32] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[14:32:32] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[14:32:33] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[14:32:33] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[14:32:33] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[June 2, 2025 at 2:32:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1300234240
[June 2, 2025 at 2:32:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1300234240
[June 2, 2025 at 2:32:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=754974720
[June 2, 2025 at 2:32:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[June 2, 2025 at 2:32:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[June 2, 2025 at 2:32:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[June 2, 2025 at 2:32:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[June 2, 2025 at 2:32:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[June 2, 2025 at 2:32:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[June 2, 2025 at 2:32:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[June 2, 2025 at 2:32:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=595591168
[June 2, 2025 at 2:32:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=595591168
[June 2, 2025 at 2:32:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=595591168
[June 2, 2025 at 2:32:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=595591168
[June 2, 2025 at 2:32:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:32:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160