Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.009s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.009s |
passed |
| testMissingContigForInterval |
0.102s |
passed |
| testReadFilterOff |
0.012s |
passed |
| testReadFilterOn |
0.013s |
passed |
| testRequiresIndexForInterval |
0.099s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.084s |
passed |
Standard error
[May 27, 2025 at 6:03:02 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
18:03:02.770 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:03:02.770 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
18:03:02.770 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
18:03:02.770 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:03:02.770 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:03:02.771 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 6:03:02 PM UTC
18:03:02.771 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:03:02.771 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:03:02.771 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:03:02.771 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:03:02.771 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:03:02.771 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:03:02.771 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
18:03:02.771 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
18:03:02.771 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
18:03:02.771 INFO TestGATKToolWithFeatures - Requester pays: disabled
18:03:02.771 INFO TestGATKToolWithFeatures - Initializing engine
18:03:02.773 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
18:03:02.774 INFO TestGATKToolWithFeatures - Done initializing engine
18:03:02.774 INFO ProgressMeter - Starting traversal
18:03:02.774 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:03:02.776 INFO ProgressMeter - unmapped 0.0 2 60000.0
18:03:02.776 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
18:03:02.776 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 6:03:02 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
18:03:02.783 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:03:02.783 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
18:03:02.783 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
18:03:02.783 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:03:02.783 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:03:02.783 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 6:03:02 PM UTC
18:03:02.783 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:03:02.783 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
18:03:02.783 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:03:02.783 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:03:02.783 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:03:02.783 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:03:02.783 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
18:03:02.783 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
18:03:02.784 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
18:03:02.784 INFO TestGATKToolWithFeatures - Requester pays: disabled
18:03:02.784 INFO TestGATKToolWithFeatures - Initializing engine
18:03:02.785 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
18:03:02.786 INFO TestGATKToolWithFeatures - Done initializing engine
18:03:02.786 INFO ProgressMeter - Starting traversal
18:03:02.786 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:03:02.788 INFO ProgressMeter - unmapped 0.0 2 60000.0
18:03:02.790 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
18:03:02.790 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 6:03:02 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 6:03:02 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 6:03:02 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000