Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.016s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.016s |
passed |
| testMissingContigForInterval |
0.115s |
passed |
| testReadFilterOff |
0.023s |
passed |
| testReadFilterOn |
0.025s |
passed |
| testRequiresIndexForInterval |
0.122s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.109s |
passed |
Standard error
[May 19, 2025 at 3:47:42 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
15:47:42.432 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:42.432 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:42.432 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:42.432 INFO TestGATKToolWithFeatures - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:42.432 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:42.432 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 3:47:42 PM GMT
15:47:42.432 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:42.432 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:42.432 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:42.433 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:42.433 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:42.433 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:42.433 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
15:47:42.433 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
15:47:42.433 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
15:47:42.433 INFO TestGATKToolWithFeatures - Requester pays: disabled
15:47:42.433 INFO TestGATKToolWithFeatures - Initializing engine
15:47:42.435 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
15:47:42.436 INFO TestGATKToolWithFeatures - Done initializing engine
15:47:42.436 INFO ProgressMeter - Starting traversal
15:47:42.436 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:47:42.438 INFO ProgressMeter - unmapped 0.0 2 60000.0
15:47:42.438 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:47:42.438 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 3:47:42 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
15:47:42.458 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:42.458 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:42.458 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:42.458 INFO TestGATKToolWithFeatures - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:42.458 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:42.458 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 3:47:42 PM GMT
15:47:42.458 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:42.458 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:42.458 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:42.458 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:42.458 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:42.459 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:42.459 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
15:47:42.459 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
15:47:42.459 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
15:47:42.459 INFO TestGATKToolWithFeatures - Requester pays: disabled
15:47:42.459 INFO TestGATKToolWithFeatures - Initializing engine
15:47:42.460 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
15:47:42.461 INFO TestGATKToolWithFeatures - Done initializing engine
15:47:42.461 INFO ProgressMeter - Starting traversal
15:47:42.461 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:47:42.463 INFO ProgressMeter - unmapped 0.0 2 60000.0
15:47:42.463 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:47:42.463 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 3:47:42 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:47:42 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:47:42 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000