Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerGroupedOnStartUnitTest
5

tests
0

failures
0

ignored
0.099s

duration
100%

successful

Tests

Test Duration Result
testIgnoreVariantsThatStartOutsideInterval 0.014s passed
testMergingTwoFilesCorrectBehavior 0.029s passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf) 0.023s passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf) 0.023s passed
testSingleFileMultisites 0.010s passed

Standard error

19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:48:11.803 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:48:11.805 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:48:11.808 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
19:48:11.808 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:48:11.808 INFO  ProgressMeter - Starting traversal
19:48:11.808 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:48:11.811 INFO  ProgressMeter -             unmapped              0.0                     4          80000.0
19:48:11.811 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:48:11.811 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.816 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:48:11.817 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:48:11.818 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:48:11.819 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:48:11.832 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:48:11.832 INFO  ProgressMeter - Starting traversal
19:48:11.832 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:48:11.833 INFO  ProgressMeter -             unmapped              0.0                    21        1260000.0
19:48:11.833 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
19:48:11.833 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.835 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:48:11.836 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.846 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:48:11.847 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:48:11.848 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:48:11.850 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
19:48:11.861 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:48:11.861 INFO  ProgressMeter - Starting traversal
19:48:11.861 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:48:11.863 INFO  ProgressMeter -             unmapped              0.0                    22         660000.0
19:48:11.863 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
19:48:11.863 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.864 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:48:11.870 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:48:11.872 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:48:11.873 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
19:48:11.885 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:48:11.885 INFO  ProgressMeter - Starting traversal
19:48:11.885 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:48:11.886 INFO  ProgressMeter -             unmapped              0.0                    20        1200000.0
19:48:11.886 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
19:48:11.886 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
19:48:11.887 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:48:11.893 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.893 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
19:48:11.893 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:48:11.893 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:48:11.893 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 7:48:11 PM UTC
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:48:11.894 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:48:11.895 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
19:48:11.897 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:48:11.897 INFO  ProgressMeter - Starting traversal
19:48:11.897 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:48:11.898 INFO  ProgressMeter -             unmapped              0.0                     7         420000.0
19:48:11.898 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
19:48:11.898 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 7:48:11 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600