Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.009s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.008s |
passed |
| testMissingContigForInterval |
0.090s |
passed |
| testReadFilterOff |
0.012s |
passed |
| testReadFilterOn |
0.013s |
passed |
| testRequiresIndexForInterval |
0.092s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.087s |
passed |
Standard error
[June 2, 2025 at 2:09:15 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
14:09:15.335 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:09:15.335 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
14:09:15.335 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
14:09:15.335 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:09:15.335 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:09:15.335 INFO TestGATKToolWithFeatures - Start Date/Time: June 2, 2025 at 2:09:15 PM UTC
14:09:15.335 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:09:15.335 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:09:15.335 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:09:15.335 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:09:15.335 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:09:15.336 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:09:15.336 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
14:09:15.336 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
14:09:15.336 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
14:09:15.336 INFO TestGATKToolWithFeatures - Requester pays: disabled
14:09:15.336 INFO TestGATKToolWithFeatures - Initializing engine
14:09:15.338 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
14:09:15.338 INFO TestGATKToolWithFeatures - Done initializing engine
14:09:15.338 INFO ProgressMeter - Starting traversal
14:09:15.338 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:09:15.339 INFO ProgressMeter - unmapped 0.0 2 120000.0
14:09:15.340 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:09:15.340 INFO TestGATKToolWithFeatures - Shutting down engine
[June 2, 2025 at 2:09:15 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
14:09:15.346 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:09:15.346 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
14:09:15.347 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
14:09:15.347 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:09:15.347 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:09:15.347 INFO TestGATKToolWithFeatures - Start Date/Time: June 2, 2025 at 2:09:15 PM UTC
14:09:15.347 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:09:15.347 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:09:15.347 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:09:15.347 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:09:15.347 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:09:15.347 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:09:15.347 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
14:09:15.347 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
14:09:15.347 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
14:09:15.348 INFO TestGATKToolWithFeatures - Requester pays: disabled
14:09:15.348 INFO TestGATKToolWithFeatures - Initializing engine
14:09:15.349 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
14:09:15.350 INFO TestGATKToolWithFeatures - Done initializing engine
14:09:15.350 INFO ProgressMeter - Starting traversal
14:09:15.350 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:09:15.352 INFO ProgressMeter - unmapped 0.0 2 60000.0
14:09:15.353 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:09:15.353 INFO TestGATKToolWithFeatures - Shutting down engine
[June 2, 2025 at 2:09:15 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
[June 2, 2025 at 2:09:15 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
[June 2, 2025 at 2:09:15 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144