Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerGroupedOnStartUnitTest
tests
failures
ignored
0.166s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIgnoreVariantsThatStartOutsideInterval	0.029s	passed
testMergingTwoFilesCorrectBehavior	0.040s	passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf)	0.039s	passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf)	0.036s	passed
testSingleFileMultisites	0.022s	passed
Standard error

20:25:21.952 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:21.952 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.952 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.952 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.952 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:25:21.953 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:25:21.956 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:25:21.959 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
20:25:21.960 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:25:21.960 INFO  ProgressMeter - Starting traversal
20:25:21.960 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:25:21.964 INFO  ProgressMeter -             unmapped              0.0                     4          60000.0
20:25:21.964 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
20:25:21.964 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.980 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:21.980 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.980 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.980 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.980 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:25:21.981 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:25:21.982 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:25:21.984 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:25:21.996 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:25:21.996 INFO  ProgressMeter - Starting traversal
20:25:21.996 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:25:21.998 INFO  ProgressMeter -             unmapped              0.0                    21         630000.0
20:25:21.998 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
20:25:21.998 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.999 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:25:22.001 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:25:22.021 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.021 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.021 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.021 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.021 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.021 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.021 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:25:22.022 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:25:22.024 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:25:22.026 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
20:25:22.041 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:25:22.041 INFO  ProgressMeter - Starting traversal
20:25:22.041 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:25:22.042 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
20:25:22.042 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
20:25:22.042 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.044 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:25:22.061 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:25:22.063 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:25:22.065 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
20:25:22.078 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:25:22.078 INFO  ProgressMeter - Starting traversal
20:25:22.078 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:25:22.079 INFO  ProgressMeter -             unmapped              0.0                    20        1200000.0
20:25:22.079 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
20:25:22.079 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.081 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:25:22.097 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.097 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.097 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.097 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.097 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.097 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:25:22.098 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:25:22.099 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
20:25:22.102 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:25:22.102 INFO  ProgressMeter - Starting traversal
20:25:22.102 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:25:22.103 INFO  ProgressMeter -             unmapped              0.0                     7         420000.0
20:25:22.103 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
20:25:22.103 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408