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

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

tests
0

failures
0

ignored
1m12.61s

duration
100%

successful

Tests

Test Duration Result
testPositiveAnnotationForOneVariantTypeIsCompletelyMissing 4.718s passed
testPositiveAnnotationsOfSpecifiedVariantTypesNotPresent 3.657s passed
testSNPOnlyModelsFromSNPOnlyAndSNPPlusIndelAnnotationsAreIdentical 7.254s passed
testValidInputs[0](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.599s 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) 6.336s passed
testValidInputs[11](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.9436869214569792521.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) 5.607s 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) 3.581s passed
testValidInputs[2](extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.9436869214569792521.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) 2.842s passed
testValidInputs[3](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.349s 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) 6.426s passed
testValidInputs[5](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed, --mode SNP --mode INDEL --python-script /tmp/isolation-forest.9436869214569792521.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) 5.601s passed
testValidInputs[6](extract.AS.snpIndel.posUn.train.snp.posOnly.IF, --mode SNP --model-backend PYTHON_IFOREST) 3.676s 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) 3.624s passed
testValidInputs[8](extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed, --mode SNP --python-script /tmp/isolation-forest.9436869214569792521.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) 2.954s passed
testValidInputs[9](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF, --mode SNP --mode INDEL --model-backend PYTHON_IFOREST) 6.385s passed

Standard output

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Standard error

15:44:00.801 INFO  HDF5Library - Trying to load HDF5 library from:
	jar:file:/gatk/gatk-package-8c12538-SNAPSHOT-local.jar!/org/broadinstitute/hdf5/libjhdf5.2.11.0.so
15:44:00.835 INFO  H5 - HDF5 library: 
15:44:00.835 INFO  H5 -  successfully loaded.
[October 23, 2025 at 3:44:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:44:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:45:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:45:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=524288000
[October 23, 2025 at 3:45:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=524288000