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

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

tests
0

failures
0

ignored
1m9.26s

duration
100%

successful

Tests

Test Duration Result
testPositiveAnnotationForOneVariantTypeIsCompletelyMissing 4.654s passed
testPositiveAnnotationsOfSpecifiedVariantTypesNotPresent 3.528s passed
testSNPOnlyModelsFromSNPOnlyAndSNPPlusIndelAnnotationsAreIdentical 6.870s passed
testValidInputs[0](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.419s 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) 6.115s passed
testValidInputs[11](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.3618490735735944763.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) 5.385s 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) 3.432s passed
testValidInputs[2](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.3618490735735944763.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) 2.744s passed
testValidInputs[3](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.046s 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) 5.951s passed
testValidInputs[5](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.3618490735735944763.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) 5.396s passed
testValidInputs[6](extract.AS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.460s 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) 3.456s passed
testValidInputs[8](extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.3618490735735944763.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) 2.715s passed
testValidInputs[9](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.093s passed

Standard output

dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found
dataset: </data/scores> and </data/scores>
0 differences found

Standard error

14:58:15.710 INFO  HDF5Library - Trying to load HDF5 library from:
	jar:file:/gatk/gatk-package-7acfd32-SNAPSHOT-local.jar!/org/broadinstitute/hdf5/libjhdf5.2.11.0.so
14:58:15.744 INFO  H5 - HDF5 library: 
14:58:15.745 INFO  H5 -  successfully loaded.
[January 7, 2026 at 2:58:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:46 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:58:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:59:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:59:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:59:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:59:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:59:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 7, 2026 at 2:59:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=524288000