Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.017s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.017s |
passed |
| testMissingContigForInterval |
0.100s |
passed |
| testReadFilterOff |
0.020s |
passed |
| testReadFilterOn |
0.019s |
passed |
| testRequiresIndexForInterval |
0.103s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.100s |
passed |
Standard error
[June 2, 2025 at 2:22:12 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
14:22:12.210 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:22:12.210 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:22:12.210 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
14:22:12.210 INFO TestGATKToolWithFeatures - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:22:12.210 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:22:12.210 INFO TestGATKToolWithFeatures - Start Date/Time: June 2, 2025 at 2:22:12 PM GMT
14:22:12.211 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:22:12.211 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:22:12.211 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:22:12.211 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:22:12.211 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:22:12.211 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:22:12.211 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
14:22:12.211 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
14:22:12.211 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
14:22:12.211 INFO TestGATKToolWithFeatures - Requester pays: disabled
14:22:12.211 INFO TestGATKToolWithFeatures - Initializing engine
14:22:12.213 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
14:22:12.214 INFO TestGATKToolWithFeatures - Done initializing engine
14:22:12.214 INFO ProgressMeter - Starting traversal
14:22:12.214 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:22:12.216 INFO ProgressMeter - unmapped 0.0 2 60000.0
14:22:12.216 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:22:12.216 INFO TestGATKToolWithFeatures - Shutting down engine
[June 2, 2025 at 2:22:12 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
14:22:12.231 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:22:12.231 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:22:12.231 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
14:22:12.231 INFO TestGATKToolWithFeatures - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:22:12.231 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:22:12.231 INFO TestGATKToolWithFeatures - Start Date/Time: June 2, 2025 at 2:22:12 PM GMT
14:22:12.231 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:22:12.231 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
14:22:12.231 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:22:12.231 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:22:12.231 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:22:12.232 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:22:12.232 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
14:22:12.232 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
14:22:12.232 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
14:22:12.232 INFO TestGATKToolWithFeatures - Requester pays: disabled
14:22:12.232 INFO TestGATKToolWithFeatures - Initializing engine
14:22:12.233 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
14:22:12.234 INFO TestGATKToolWithFeatures - Done initializing engine
14:22:12.234 INFO ProgressMeter - Starting traversal
14:22:12.234 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:22:12.236 INFO ProgressMeter - unmapped 0.0 2 60000.0
14:22:12.236 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:22:12.236 INFO TestGATKToolWithFeatures - Shutting down engine
[June 2, 2025 at 2:22:12 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:22:12 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 2, 2025 at 2:22:12 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000