Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.023s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.023s |
passed |
| testMissingContigForInterval |
0.103s |
passed |
| testReadFilterOff |
0.020s |
passed |
| testReadFilterOn |
0.020s |
passed |
| testRequiresIndexForInterval |
0.091s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.087s |
passed |
Standard error
[May 19, 2025 at 7:00:42 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
19:00:42.081 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:00:42.081 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:00:42.081 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
19:00:42.081 INFO TestGATKToolWithFeatures - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:00:42.082 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:00:42.082 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 7:00:42 PM GMT
19:00:42.082 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:00:42.082 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:00:42.082 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:00:42.082 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:00:42.082 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:00:42.082 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:00:42.082 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
19:00:42.082 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
19:00:42.082 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
19:00:42.082 INFO TestGATKToolWithFeatures - Requester pays: disabled
19:00:42.082 INFO TestGATKToolWithFeatures - Initializing engine
19:00:42.084 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
19:00:42.085 INFO TestGATKToolWithFeatures - Done initializing engine
19:00:42.085 INFO ProgressMeter - Starting traversal
19:00:42.085 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:00:42.086 INFO ProgressMeter - unmapped 0.0 2 120000.0
19:00:42.086 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
19:00:42.086 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 7:00:42 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
19:00:42.101 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:00:42.101 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:00:42.102 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
19:00:42.102 INFO TestGATKToolWithFeatures - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:00:42.102 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:00:42.102 INFO TestGATKToolWithFeatures - Start Date/Time: May 19, 2025 at 7:00:42 PM GMT
19:00:42.102 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:00:42.102 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
19:00:42.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:00:42.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:00:42.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:00:42.102 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:00:42.102 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
19:00:42.102 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
19:00:42.102 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
19:00:42.102 INFO TestGATKToolWithFeatures - Requester pays: disabled
19:00:42.102 INFO TestGATKToolWithFeatures - Initializing engine
19:00:42.104 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
19:00:42.104 INFO TestGATKToolWithFeatures - Done initializing engine
19:00:42.104 INFO ProgressMeter - Starting traversal
19:00:42.105 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:00:42.107 INFO ProgressMeter - unmapped 0.0 2 120000.0
19:00:42.107 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
19:00:42.107 INFO TestGATKToolWithFeatures - Shutting down engine
[May 19, 2025 at 7:00:42 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
[May 19, 2025 at 7:00:42 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144
[May 19, 2025 at 7:00:42 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=622854144