Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest
Tests
Test |
Duration |
Result |
testIgnoreVariantsThatStartOutsideInterval |
0.016s |
passed |
testMergingTwoFilesCorrectBehavior |
0.036s |
passed |
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf) |
0.027s |
passed |
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf) |
0.024s |
passed |
testSingleFileMultisites |
0.011s |
passed |
Standard error
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.811 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:33:07.812 INFO DummyExampleGroupingMultiVariantWalker - Initializing engine
20:33:07.814 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:33:07.816 INFO IntervalArgumentCollection - Processing 41 bp from intervals
20:33:07.816 INFO DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:33:07.816 INFO ProgressMeter - Starting traversal
20:33:07.816 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:33:07.819 INFO ProgressMeter - unmapped 0.0 4 80000.0
20:33:07.819 INFO ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
20:33:07.819 INFO DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.825 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:33:07.826 INFO DummyExampleGroupingMultiVariantWalker - Initializing engine
20:33:07.827 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:33:07.834 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:33:07.846 INFO DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:33:07.846 INFO ProgressMeter - Starting traversal
20:33:07.846 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:33:07.848 INFO ProgressMeter - unmapped 0.0 21 630000.0
20:33:07.848 INFO ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
20:33:07.848 INFO DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.849 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:33:07.851 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.862 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.863 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.863 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.863 INFO DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:33:07.863 INFO DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:33:07.863 INFO DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:33:07.863 INFO DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:33:07.863 INFO DummyExampleGroupingMultiVariantWalker - Initializing engine
20:33:07.864 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:33:07.866 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
20:33:07.879 INFO DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:33:07.880 INFO ProgressMeter - Starting traversal
20:33:07.880 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:33:07.881 INFO ProgressMeter - unmapped 0.0 22 1320000.0
20:33:07.881 INFO ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
20:33:07.881 INFO DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.883 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:33:07.890 INFO DummyExampleGroupingMultiVariantWalker - Initializing engine
20:33:07.892 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:33:07.893 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
20:33:07.905 INFO DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:33:07.905 INFO ProgressMeter - Starting traversal
20:33:07.905 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:33:07.907 INFO ProgressMeter - unmapped 0.0 20 1200000.0
20:33:07.907 INFO ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
20:33:07.907 INFO DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
20:33:07.908 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:33:07 PM UTC
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:33:07.914 INFO DummyExampleGroupingMultiVariantWalker - Initializing engine
20:33:07.916 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
20:33:07.918 INFO DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:33:07.918 INFO ProgressMeter - Starting traversal
20:33:07.918 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:33:07.919 INFO ProgressMeter - unmapped 0.0 7 420000.0
20:33:07.919 INFO ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
20:33:07.919 INFO DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:33:07 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600