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

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

tests
0

failures
0

ignored
1m9.59s

duration
100%

successful

Tests

Test Duration Result
testPositiveAnnotationForOneVariantTypeIsCompletelyMissing 4.678s passed
testPositiveAnnotationsOfSpecifiedVariantTypesNotPresent 3.514s passed
testSNPOnlyModelsFromSNPOnlyAndSNPPlusIndelAnnotationsAreIdentical 6.991s passed
testValidInputs[0](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.468s 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) 6.079s passed
testValidInputs[11](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.7468415317507001242.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) 5.391s 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) 3.430s passed
testValidInputs[2](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.7468415317507001242.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) 2.742s passed
testValidInputs[3](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.106s 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) 6.114s passed
testValidInputs[5](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.7468415317507001242.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) 5.343s passed
testValidInputs[6](extract.AS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.443s 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) 3.475s passed
testValidInputs[8](extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.7468415317507001242.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) 2.739s passed
testValidInputs[9](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.081s passed

Standard output

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Standard error

18:09:10.033 INFO  HDF5Library - Trying to load HDF5 library from:
	jar:file:/gatk/gatk-package-54faf8a-SNAPSHOT-local.jar!/org/broadinstitute/hdf5/libjhdf5.2.11.0.so
18:09:10.074 INFO  H5 - HDF5 library: 
18:09:10.074 INFO  H5 -  successfully loaded.
[October 27, 2025 at 6:09:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:09:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:10:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:10:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:10:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 6:10:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=524288000