Test Summary
|
96%
successful |
Failed tests
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[0](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[1](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[2](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.164998051459177152.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[3](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.164998051459177152.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[4](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[5](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[6](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.164998051459177152.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[7](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.164998051459177152.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
Packages
| Package | Tests | Failures | Ignored | Duration | Success rate |
|---|---|---|---|---|---|
| org.broadinstitute.hellbender.tools.copynumber | 39 | 0 | 0 | 12m11.68s | 100% |
| org.broadinstitute.hellbender.tools.copynumber.plotting | 6 | 0 | 0 | 3.336s | 100% |
| org.broadinstitute.hellbender.tools.examples | 6 | 0 | 0 | 2.145s | 100% |
| org.broadinstitute.hellbender.tools.spark.pipelines.metrics | 31 | 0 | 0 | 16.175s | 100% |
| org.broadinstitute.hellbender.tools.walkers.bqsr | 6 | 0 | 0 | 11.149s | 100% |
| org.broadinstitute.hellbender.tools.walkers.varianteval | 1 | 0 | 0 | 2.680s | 100% |
| org.broadinstitute.hellbender.tools.walkers.vqsr | 2 | 0 | 0 | 43.784s | 100% |
| org.broadinstitute.hellbender.tools.walkers.vqsr.scalable | 41 | 8 | 0 | 1m25.10s | 80% |
| org.broadinstitute.hellbender.utils.R | 10 | 0 | 0 | 1.301s | 100% |
| org.broadinstitute.hellbender.utils.python | 70 | 0 | 0 | 15.403s | 100% |
| org.broadinstitute.hellbender.utils.runtime | 11 | 0 | 0 | 0.420s | 100% |