Class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.vqsr.scalable > TrainVariantAnnotationsModelIntegrationTest
15

tests
0

failures
0

ignored
1m16.04s

duration
100%

successful

Tests

Test Duration Result
testPositiveAnnotationForOneVariantTypeIsCompletelyMissing 5.403s passed
testPositiveAnnotationsOfSpecifiedVariantTypesNotPresent 3.988s passed
testSNPOnlyModelsFromSNPOnlyAndSNPPlusIndelAnnotationsAreIdentical 7.179s passed
testValidInputs[0](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.557s passed
testValidInputs[10](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_IFOREST) 6.128s passed
testValidInputs[11](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.10669623667103286453.py --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_SCRIPT) 5.727s passed
testValidInputs[1](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_IFOREST) 4.127s passed
testValidInputs[2](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.10669623667103286453.py --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_SCRIPT) 3.756s passed
testValidInputs[3](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.205s passed
testValidInputs[4](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_IFOREST) 5.958s passed
testValidInputs[5](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.10669623667103286453.py --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_SCRIPT) 5.848s passed
testValidInputs[6](extract.AS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 4.045s passed
testValidInputs[7](extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_IFOREST) 4.211s passed
testValidInputs[8](extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.10669623667103286453.py --hyperparameters-json /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json --model-backend PYTHON_SCRIPT) 3.462s passed
testValidInputs[9](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.446s passed

Standard output

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Standard error

17:46:04.265 INFO  HDF5Library - Trying to load HDF5 library from:
	jar:file:/gatk/gatk-package-e7de3f7-SNAPSHOT-local.jar!/org/broadinstitute/hdf5/libjhdf5.2.11.0.so
17:46:04.311 INFO  H5 - HDF5 library: 
17:46:04.312 INFO  H5 -  successfully loaded.
[January 5, 2026 at 5:46:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:46:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:47:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:47:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:47:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:47:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=524288000