Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.009s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.008s |
passed |
| testMissingContigForInterval |
0.089s |
passed |
| testReadFilterOff |
0.011s |
passed |
| testReadFilterOn |
0.011s |
passed |
| testRequiresIndexForInterval |
0.092s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.082s |
passed |
Standard error
[March 28, 2025 at 10:33:06 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
22:33:06.405 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:33:06.405 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
22:33:06.405 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
22:33:06.405 INFO TestGATKToolWithFeatures - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:33:06.405 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:33:06.405 INFO TestGATKToolWithFeatures - Start Date/Time: March 28, 2025 at 10:33:06 PM UTC
22:33:06.405 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:33:06.406 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:33:06.406 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:33:06.406 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:33:06.406 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:33:06.406 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:33:06.406 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
22:33:06.406 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
22:33:06.406 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
22:33:06.406 INFO TestGATKToolWithFeatures - Requester pays: disabled
22:33:06.406 INFO TestGATKToolWithFeatures - Initializing engine
22:33:06.408 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
22:33:06.409 INFO TestGATKToolWithFeatures - Done initializing engine
22:33:06.409 INFO ProgressMeter - Starting traversal
22:33:06.409 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
22:33:06.410 INFO ProgressMeter - unmapped 0.0 2 120000.0
22:33:06.410 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
22:33:06.410 INFO TestGATKToolWithFeatures - Shutting down engine
[March 28, 2025 at 10:33:06 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
22:33:06.416 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:33:06.416 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
22:33:06.417 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
22:33:06.417 INFO TestGATKToolWithFeatures - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:33:06.417 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:33:06.417 INFO TestGATKToolWithFeatures - Start Date/Time: March 28, 2025 at 10:33:06 PM UTC
22:33:06.417 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:33:06.417 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
22:33:06.417 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:33:06.417 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:33:06.417 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:33:06.417 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:33:06.417 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
22:33:06.417 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
22:33:06.417 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
22:33:06.417 INFO TestGATKToolWithFeatures - Requester pays: disabled
22:33:06.417 INFO TestGATKToolWithFeatures - Initializing engine
22:33:06.418 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
22:33:06.419 INFO TestGATKToolWithFeatures - Done initializing engine
22:33:06.419 INFO ProgressMeter - Starting traversal
22:33:06.419 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
22:33:06.421 INFO ProgressMeter - unmapped 0.0 2 60000.0
22:33:06.421 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
22:33:06.421 INFO TestGATKToolWithFeatures - Shutting down engine
[March 28, 2025 at 10:33:06 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:33:06 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:33:06 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000