Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerGroupedOnStartUnitTest
tests
failures
ignored
0.219s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIgnoreVariantsThatStartOutsideInterval	0.035s	passed
testMergingTwoFilesCorrectBehavior	0.061s	passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf)	0.049s	passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf)	0.047s	passed
testSingleFileMultisites	0.027s	passed
Standard error

20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:47:49 PM GMT
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:47:49.864 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:47:49.867 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:47:49.871 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
20:47:49.871 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:47:49.871 INFO  ProgressMeter - Starting traversal
20:47:49.871 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:47:49.875 INFO  ProgressMeter -             unmapped              0.0                     4          60000.0
20:47:49.875 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
20:47:49.875 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:47:49 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:49.902 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:47:49 PM GMT
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:47:49.903 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:47:49.905 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:47:49.907 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:47:49.926 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:47:49.926 INFO  ProgressMeter - Starting traversal
20:47:49.926 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:47:49.927 INFO  ProgressMeter -             unmapped              0.0                    21        1260000.0
20:47:49.927 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
20:47:49.928 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:47:49 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:49.929 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:47:49.931 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:47:49 PM GMT
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:47:49.959 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:47:49.961 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:47:49.963 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
20:47:49.981 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:47:49.981 INFO  ProgressMeter - Starting traversal
20:47:49.981 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:47:49.983 INFO  ProgressMeter -             unmapped              0.0                    22         660000.0
20:47:49.983 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
20:47:49.983 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:47:49 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:49.984 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:47:50.007 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:47:50.009 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:47:50.011 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
20:47:50.029 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:47:50.029 INFO  ProgressMeter - Starting traversal
20:47:50.029 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:47:50.030 INFO  ProgressMeter -             unmapped              0.0                    20        1200000.0
20:47:50.030 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
20:47:50.030 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.032 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:47:50.054 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:47:50.055 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:47:50.057 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
20:47:50.059 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:47:50.059 INFO  ProgressMeter - Starting traversal
20:47:50.059 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:47:50.060 INFO  ProgressMeter -             unmapped              0.0                     7         420000.0
20:47:50.060 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
20:47:50.060 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912