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

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

tests
0

failures
0

ignored
1m7.23s

duration
100%

successful

Tests

Test Duration Result
testPositiveAnnotationForOneVariantTypeIsCompletelyMissing 4.660s passed
testPositiveAnnotationsOfSpecifiedVariantTypesNotPresent 3.388s passed
testSNPOnlyModelsFromSNPOnlyAndSNPPlusIndelAnnotationsAreIdentical 6.676s passed
testValidInputs[0](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.358s 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) 5.891s passed
testValidInputs[11](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.1720826591666807118.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) 5.167s 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) 3.329s passed
testValidInputs[2](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.1720826591666807118.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) 2.628s passed
testValidInputs[3](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 5.919s 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) 5.902s passed
testValidInputs[5](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.1720826591666807118.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) 5.138s passed
testValidInputs[6](extract.AS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.336s 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) 3.334s passed
testValidInputs[8](extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.1720826591666807118.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) 2.637s passed
testValidInputs[9](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 5.871s 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

17:54:49.131 INFO  HDF5Library - Trying to load HDF5 library from:
	jar:file:/gatk/gatk-package-30ded87-SNAPSHOT-local.jar!/org/broadinstitute/hdf5/libjhdf5.2.11.0.so
17:54:49.170 INFO  H5 - HDF5 library: 
17:54:49.170 INFO  H5 -  successfully loaded.
[January 5, 2026 at 5:54:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:54:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:45 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[January 5, 2026 at 5:55:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=524288000