Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

5

tests

0

failures

0

ignored

0.114s

duration

100%

successful

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