Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.019s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.023s |
passed |
| testMissingContigForInterval |
0.114s |
passed |
| testReadFilterOff |
0.023s |
passed |
| testReadFilterOn |
0.021s |
passed |
| testRequiresIndexForInterval |
0.123s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.118s |
passed |
Standard error
[May 27, 2025 at 6:16:55 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
18:16:55.528 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:16:55.528 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:16:55.529 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
18:16:55.529 INFO TestGATKToolWithFeatures - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:16:55.529 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:16:55.529 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 6:16:55 PM GMT
18:16:55.529 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:16:55.529 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:16:55.529 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:16:55.529 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:16:55.529 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:16:55.529 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:16:55.529 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
18:16:55.529 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
18:16:55.529 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
18:16:55.529 INFO TestGATKToolWithFeatures - Requester pays: disabled
18:16:55.529 INFO TestGATKToolWithFeatures - Initializing engine
18:16:55.532 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
18:16:55.533 INFO TestGATKToolWithFeatures - Done initializing engine
18:16:55.533 INFO ProgressMeter - Starting traversal
18:16:55.533 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:16:55.534 INFO ProgressMeter - unmapped 0.0 2 120000.0
18:16:55.534 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
18:16:55.535 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 6:16:55 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
18:16:55.551 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:16:55.552 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:16:55.552 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
18:16:55.552 INFO TestGATKToolWithFeatures - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:16:55.552 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:16:55.552 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 6:16:55 PM GMT
18:16:55.552 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:16:55.552 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:16:55.552 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:16:55.552 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:16:55.552 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:16:55.552 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:16:55.552 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
18:16:55.552 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
18:16:55.552 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
18:16:55.552 INFO TestGATKToolWithFeatures - Requester pays: disabled
18:16:55.552 INFO TestGATKToolWithFeatures - Initializing engine
18:16:55.554 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
18:16:55.555 INFO TestGATKToolWithFeatures - Done initializing engine
18:16:55.555 INFO ProgressMeter - Starting traversal
18:16:55.555 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:16:55.557 INFO ProgressMeter - unmapped 0.0 2 60000.0
18:16:55.557 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
18:16:55.557 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 6:16:55 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 6:16:55 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 6:16:55 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000