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

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

tests

failures

ignored

13.600s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testASAnnotationsAndSubsetting	3.692s	passed
testAddedHcAsAnnotations	0.152s	passed
testAggressiveQualFiltering	0.109s	passed
testContiguityWithSpanningDels	0.433s	passed
testDragenGvcfs	0.224s	passed
testFilters	0.228s	passed
testFirstPositionOnContigNotDropped	0.161s	passed
testGVCFReblockingIsContiguous	4.727s	passed
testHomRefCalls	0.170s	passed
testLeftContigBoundary	0.184s	passed
testMQHeadersAreUpdated	0.214s	passed
testMixedSamples	0.164s	passed
testMovingFilters	0.222s	passed
testMultipleInputs	0.344s	passed
testNewCompressionScheme	0.107s	passed
testNoCallGenotypes	0.156s	passed
testNoCallWhenGQ0InNonRefAllele	0.153s	passed
testNonGVCFInput	0.099s	passed
testNonRefADCorrection	0.103s	passed
testOneSampleAsForGnomAD	0.101s	passed
testOverlappingDeletions	0.255s	passed
testPosteriorDisagreementNeedingSubset	0.150s	passed
testRawMQInput	0.127s	passed
testReReblocking	0.214s	passed
testRemovingAnnotationFromEmptyAttributes	0.157s	passed
testRemovingFormatAnnotations	0.210s	passed
testSpanDelRegression	0.110s	passed
testTreeScoreThreshold	0.106s	passed
testTreeScoreWithNoAnnotation	0.101s	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, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)	0.099s	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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.163s	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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.165s	passed

Standard output

--------------------------------------------------------------------------------
[16:12:25] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
--------------------------------------------------------------------------------
[16:12:25] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
--------------------------------------------------------------------------------
[16:12:28] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
--------------------------------------------------------------------------------
[16:12:36] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
--------------------------------------------------------------------------------
[16:12:36] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
--------------------------------------------------------------------------------
[16:12:36] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
--------------------------------------------------------------------------------
[16:12:36] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
--------------------------------------------------------------------------------
[16:12:37] Executing test ReblockGVCFIntegrationTest:testRawMQInput
--------------------------------------------------------------------------------
[16:12:38] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
--------------------------------------------------------------------------------
[16:12:38] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
--------------------------------------------------------------------------------
[16:12:38] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 19, 2025 at 4:12:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000