Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.008s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.010s |
passed |
| testMissingContigForInterval |
0.098s |
passed |
| testReadFilterOff |
0.011s |
passed |
| testReadFilterOn |
0.013s |
passed |
| testRequiresIndexForInterval |
0.100s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.085s |
passed |
Standard error
[May 19, 2025 at 3:32:14 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
15:32:14.715 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:32:14.715 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
15:32:14.715 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
15:32:14.715 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:32:14.715 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:32:14.715 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 3:32:14 PM UTC
15:32:14.715 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:32:14.715 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:32:14.715 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:32:14.715 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:32:14.715 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:32:14.715 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:32:14.715 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
15:32:14.716 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
15:32:14.716 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
15:32:14.716 INFO TestGATKToolWithFeatures - Requester pays: disabled
15:32:14.716 INFO TestGATKToolWithFeatures - Initializing engine
15:32:14.717 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
15:32:14.718 INFO TestGATKToolWithFeatures - Done initializing engine
15:32:14.718 INFO ProgressMeter - Starting traversal
15:32:14.718 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:32:14.720 INFO ProgressMeter - unmapped 0.0 2 120000.0
15:32:14.720 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:32:14.720 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 3:32:14 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
15:32:14.727 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:32:14.727 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
15:32:14.727 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
15:32:14.727 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:32:14.727 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:32:14.727 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 3:32:14 PM UTC
15:32:14.727 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:32:14.727 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:32:14.727 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:32:14.727 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:32:14.727 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:32:14.727 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:32:14.727 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
15:32:14.728 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
15:32:14.728 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
15:32:14.728 INFO TestGATKToolWithFeatures - Requester pays: disabled
15:32:14.728 INFO TestGATKToolWithFeatures - Initializing engine
15:32:14.729 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
15:32:14.730 INFO TestGATKToolWithFeatures - Done initializing engine
15:32:14.730 INFO ProgressMeter - Starting traversal
15:32:14.730 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:32:14.732 INFO ProgressMeter - unmapped 0.0 2 60000.0
15:32:14.732 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:32:14.733 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 3:32:14 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:32:14 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:32:14 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000