Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.019s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.016s |
passed |
| testMissingContigForInterval |
0.107s |
passed |
| testReadFilterOff |
0.026s |
passed |
| testReadFilterOn |
0.024s |
passed |
| testRequiresIndexForInterval |
0.115s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.102s |
passed |
Standard error
[May 27, 2025 at 4:36:25 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
16:36:25.656 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
16:36:25.656 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:36:25.656 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
16:36:25.656 INFO TestGATKToolWithFeatures - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:36:25.656 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:36:25.656 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 4:36:25 PM GMT
16:36:25.656 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
16:36:25.656 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
16:36:25.657 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:36:25.657 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:36:25.657 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:36:25.657 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:36:25.657 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
16:36:25.657 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
16:36:25.657 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
16:36:25.657 INFO TestGATKToolWithFeatures - Requester pays: disabled
16:36:25.657 INFO TestGATKToolWithFeatures - Initializing engine
16:36:25.659 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
16:36:25.660 INFO TestGATKToolWithFeatures - Done initializing engine
16:36:25.660 INFO ProgressMeter - Starting traversal
16:36:25.660 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:36:25.661 INFO ProgressMeter - unmapped 0.0 2 120000.0
16:36:25.661 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
16:36:25.661 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 4:36:25 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
16:36:25.680 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
16:36:25.680 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:36:25.680 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
16:36:25.680 INFO TestGATKToolWithFeatures - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:36:25.680 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:36:25.680 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 4:36:25 PM GMT
16:36:25.680 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
16:36:25.680 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
16:36:25.680 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:36:25.680 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:36:25.680 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:36:25.680 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:36:25.680 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
16:36:25.680 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
16:36:25.680 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
16:36:25.681 INFO TestGATKToolWithFeatures - Requester pays: disabled
16:36:25.681 INFO TestGATKToolWithFeatures - Initializing engine
16:36:25.682 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
16:36:25.683 INFO TestGATKToolWithFeatures - Done initializing engine
16:36:25.683 INFO ProgressMeter - Starting traversal
16:36:25.683 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:36:25.686 INFO ProgressMeter - unmapped 0.0 2 60000.0
16:36:25.686 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
16:36:25.686 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 4:36:25 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 4:36:25 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 4:36:25 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000