Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.008s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.008s |
passed |
| testMissingContigForInterval |
0.077s |
passed |
| testReadFilterOff |
0.009s |
passed |
| testReadFilterOn |
0.011s |
passed |
| testRequiresIndexForInterval |
0.072s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.082s |
passed |
Standard error
[May 27, 2025 at 1:37:18 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
13:37:18.824 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:37:18.824 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
13:37:18.824 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
13:37:18.824 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:37:18.824 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:37:18.825 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 1:37:18 PM UTC
13:37:18.825 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:37:18.825 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:37:18.825 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:37:18.825 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:37:18.825 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:37:18.825 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:37:18.825 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
13:37:18.825 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
13:37:18.825 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
13:37:18.825 INFO TestGATKToolWithFeatures - Requester pays: disabled
13:37:18.825 INFO TestGATKToolWithFeatures - Initializing engine
13:37:18.827 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
13:37:18.828 INFO TestGATKToolWithFeatures - Done initializing engine
13:37:18.828 INFO ProgressMeter - Starting traversal
13:37:18.828 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:37:18.829 INFO ProgressMeter - unmapped 0.0 2 120000.0
13:37:18.829 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
13:37:18.829 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 1:37:18 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
13:37:18.835 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:37:18.835 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
13:37:18.835 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
13:37:18.835 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:37:18.835 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:37:18.835 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 1:37:18 PM UTC
13:37:18.835 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:37:18.835 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:37:18.835 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:37:18.835 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:37:18.835 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:37:18.836 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:37:18.836 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
13:37:18.836 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
13:37:18.836 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
13:37:18.836 INFO TestGATKToolWithFeatures - Requester pays: disabled
13:37:18.836 INFO TestGATKToolWithFeatures - Initializing engine
13:37:18.838 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
13:37:18.838 INFO TestGATKToolWithFeatures - Done initializing engine
13:37:18.838 INFO ProgressMeter - Starting traversal
13:37:18.838 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:37:18.840 INFO ProgressMeter - unmapped 0.0 2 60000.0
13:37:18.841 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
13:37:18.841 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 1:37:18 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 1:37:18 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 1:37:18 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000