Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerGroupedOnStartUnitTest
tests
failures
ignored
0.152s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIgnoreVariantsThatStartOutsideInterval	0.031s	passed
testMergingTwoFilesCorrectBehavior	0.037s	passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf)	0.031s	passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf)	0.032s	passed
testSingleFileMultisites	0.021s	passed
Standard error

22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:03:39.019 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:03:39.021 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:03:39.024 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
22:03:39.025 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:03:39.025 INFO  ProgressMeter - Starting traversal
22:03:39.025 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:03:39.028 INFO  ProgressMeter -             unmapped              0.0                     4         120000.0
22:03:39.028 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
22:03:39.028 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:03:39.043 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:03:39.044 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:03:39.046 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:03:39.057 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:03:39.057 INFO  ProgressMeter - Starting traversal
22:03:39.057 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:03:39.058 INFO  ProgressMeter -             unmapped              0.0                    21        1260000.0
22:03:39.058 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
22:03:39.058 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.059 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:03:39.061 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:03:39.079 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:03:39.080 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:03:39.081 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:03:39.083 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
22:03:39.093 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:03:39.093 INFO  ProgressMeter - Starting traversal
22:03:39.093 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:03:39.094 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
22:03:39.094 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
22:03:39.094 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.095 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:03:39.111 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:03:39.112 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:03:39.115 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
22:03:39.125 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:03:39.125 INFO  ProgressMeter - Starting traversal
22:03:39.125 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:03:39.126 INFO  ProgressMeter -             unmapped              0.0                    20        1200000.0
22:03:39.126 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
22:03:39.126 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.127 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:03:39.142 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:03:39.144 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
22:03:39.147 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:03:39.147 INFO  ProgressMeter - Starting traversal
22:03:39.147 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:03:39.147 INFO  ProgressMeter -             unmapped              0.0                     7         Infinity
22:03:39.147 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
22:03:39.147 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968