Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.016s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.017s |
passed |
| testMissingContigForInterval |
0.094s |
passed |
| testReadFilterOff |
0.020s |
passed |
| testReadFilterOn |
0.020s |
passed |
| testRequiresIndexForInterval |
0.094s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.095s |
passed |
Standard error
[May 27, 2025 at 3:47:17 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
15:47:17.553 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:17.553 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:47:17.553 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:17.553 INFO TestGATKToolWithFeatures - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:47:17.553 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:17.553 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 3:47:17 PM GMT
15:47:17.553 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:17.553 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:17.553 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:17.553 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:17.554 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:17.554 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:17.554 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
15:47:17.554 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
15:47:17.554 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
15:47:17.554 INFO TestGATKToolWithFeatures - Requester pays: disabled
15:47:17.554 INFO TestGATKToolWithFeatures - Initializing engine
15:47:17.556 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
15:47:17.557 INFO TestGATKToolWithFeatures - Done initializing engine
15:47:17.557 INFO ProgressMeter - Starting traversal
15:47:17.557 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:47:17.558 INFO ProgressMeter - unmapped 0.0 2 120000.0
15:47:17.558 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:47:17.558 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 3:47:17 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
15:47:17.573 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:17.573 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
15:47:17.574 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:17.574 INFO TestGATKToolWithFeatures - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
15:47:17.574 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:17.574 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 3:47:17 PM GMT
15:47:17.574 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:17.574 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
15:47:17.574 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:17.574 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:17.574 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:17.574 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:17.574 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
15:47:17.574 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
15:47:17.574 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
15:47:17.574 INFO TestGATKToolWithFeatures - Requester pays: disabled
15:47:17.574 INFO TestGATKToolWithFeatures - Initializing engine
15:47:17.576 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
15:47:17.577 INFO TestGATKToolWithFeatures - Done initializing engine
15:47:17.577 INFO ProgressMeter - Starting traversal
15:47:17.577 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:47:17.579 INFO ProgressMeter - unmapped 0.0 2 60000.0
15:47:17.579 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:47:17.579 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 3:47:17 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:47:17 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 3:47:17 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000