Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.018s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.018s |
passed |
| testMissingContigForInterval |
0.111s |
passed |
| testReadFilterOff |
0.022s |
passed |
| testReadFilterOn |
0.020s |
passed |
| testRequiresIndexForInterval |
0.113s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.104s |
passed |
Standard error
[June 12, 2025 at 8:48:06 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:48:06.283 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:48:06.283 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
20:48:06.283 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:48:06.283 INFO TestGATKToolWithFeatures - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
20:48:06.283 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:48:06.283 INFO TestGATKToolWithFeatures - Start Date/Time: June 12, 2025 at 8:48:06 PM GMT
20:48:06.284 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:48:06.284 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:48:06.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:48:06.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:48:06.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:48:06.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:48:06.284 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:48:06.284 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:48:06.284 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:48:06.284 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:48:06.284 INFO TestGATKToolWithFeatures - Initializing engine
20:48:06.286 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
20:48:06.287 INFO TestGATKToolWithFeatures - Done initializing engine
20:48:06.287 INFO ProgressMeter - Starting traversal
20:48:06.288 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:48:06.289 INFO ProgressMeter - unmapped 0.0 2 120000.0
20:48:06.289 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
20:48:06.289 INFO TestGATKToolWithFeatures - Shutting down engine
[June 12, 2025 at 8:48:06 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:48:06.305 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:48:06.305 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
20:48:06.305 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:48:06.305 INFO TestGATKToolWithFeatures - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
20:48:06.306 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:48:06.306 INFO TestGATKToolWithFeatures - Start Date/Time: June 12, 2025 at 8:48:06 PM GMT
20:48:06.306 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:48:06.306 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:48:06.306 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:48:06.306 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:48:06.306 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:48:06.306 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:48:06.306 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:48:06.306 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:48:06.306 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:48:06.306 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:48:06.306 INFO TestGATKToolWithFeatures - Initializing engine
20:48:06.307 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
20:48:06.308 INFO TestGATKToolWithFeatures - Done initializing engine
20:48:06.308 INFO ProgressMeter - Starting traversal
20:48:06.308 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:48:06.310 INFO ProgressMeter - unmapped 0.0 2 60000.0
20:48:06.310 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
20:48:06.310 INFO TestGATKToolWithFeatures - Shutting down engine
[June 12, 2025 at 8:48:06 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[June 12, 2025 at 8:48:06 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:48:06 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000