Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.009s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.007s |
passed |
| testMissingContigForInterval |
0.089s |
passed |
| testReadFilterOff |
0.021s |
passed |
| testReadFilterOn |
0.014s |
passed |
| testRequiresIndexForInterval |
0.086s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.074s |
passed |
Standard error
[June 12, 2025 at 8:34:00 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=664797184
20:34:00.864 INFO BlockManagerInfo - Removed broadcast_3_piece0 on localhost:35023 in memory (size: 429.0 B, free: 1919.2 MiB)
20:34:00.866 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:34:00.866 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
20:34:00.866 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:34:00.866 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:34:00.866 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:34:00.866 INFO TestGATKToolWithFeatures - Start Date/Time: June 12, 2025 at 8:34:00 PM UTC
20:34:00.866 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:34:00.866 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:34:00.867 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:34:00.867 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:34:00.867 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:34:00.868 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:34:00.868 INFO BlockManagerInfo - Removed broadcast_9_piece0 on localhost:35023 in memory (size: 427.0 B, free: 1919.2 MiB)
20:34:00.868 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:34:00.868 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:34:00.869 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:34:00.870 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:34:00.870 INFO TestGATKToolWithFeatures - Initializing engine
20:34:00.872 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
20:34:00.872 INFO BlockManagerInfo - Removed broadcast_4_piece0 on localhost:35023 in memory (size: 263.8 KiB, free: 1919.5 MiB)
20:34:00.875 INFO BlockManagerInfo - Removed broadcast_2_piece0 on localhost:35023 in memory (size: 429.0 B, free: 1919.5 MiB)
20:34:00.875 INFO TestGATKToolWithFeatures - Done initializing engine
20:34:00.875 INFO ProgressMeter - Starting traversal
20:34:00.875 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:34:00.877 INFO ProgressMeter - unmapped 0.0 2 60000.0
20:34:00.877 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
20:34:00.877 INFO TestGATKToolWithFeatures - Shutting down engine
[June 12, 2025 at 8:34:00 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=664797184
20:34:00.880 INFO BlockManagerInfo - Removed broadcast_10_piece0 on localhost:35023 in memory (size: 263.9 KiB, free: 1919.8 MiB)
20:34:00.884 INFO BlockManagerInfo - Removed broadcast_0_piece0 on localhost:35023 in memory (size: 63.7 KiB, free: 1919.8 MiB)
20:34:00.885 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:34:00.885 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
20:34:00.885 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
20:34:00.885 INFO TestGATKToolWithFeatures - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:34:00.885 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:34:00.885 INFO TestGATKToolWithFeatures - Start Date/Time: June 12, 2025 at 8:34:00 PM UTC
20:34:00.886 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:34:00.886 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
20:34:00.886 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:34:00.886 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:34:00.886 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:34:00.886 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:34:00.886 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
20:34:00.886 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
20:34:00.886 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
20:34:00.886 INFO TestGATKToolWithFeatures - Requester pays: disabled
20:34:00.886 INFO TestGATKToolWithFeatures - Initializing engine
20:34:00.888 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
20:34:00.889 INFO TestGATKToolWithFeatures - Done initializing engine
20:34:00.889 INFO ProgressMeter - Starting traversal
20:34:00.889 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:34:00.889 INFO BlockManagerInfo - Removed broadcast_5_piece0 on localhost:35023 in memory (size: 63.7 KiB, free: 1919.9 MiB)
20:34:00.891 INFO ProgressMeter - unmapped 0.0 2 60000.0
20:34:00.891 INFO BlockManagerInfo - Removed broadcast_6_piece0 on localhost:35023 in memory (size: 63.7 KiB, free: 1919.9 MiB)
20:34:00.891 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
20:34:00.892 INFO TestGATKToolWithFeatures - Shutting down engine
[June 12, 2025 at 8:34:00 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=664797184
20:34:00.899 INFO BlockManagerInfo - Removed broadcast_8_piece0 on localhost:35023 in memory (size: 427.0 B, free: 1919.9 MiB)
20:34:00.910 INFO BlockManagerInfo - Removed broadcast_1_piece0 on localhost:35023 in memory (size: 63.7 KiB, free: 1920.0 MiB)
[June 12, 2025 at 8:34:00 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=664797184
[June 12, 2025 at 8:34:01 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=664797184