Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

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

tests
0

failures
0

ignored
0.170s

duration
100%

successful

Tests

Test Duration Result
testIgnoreVariantsThatStartOutsideInterval 0.026s passed
testMergingTwoFilesCorrectBehavior 0.044s 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) 0.038s passed
testSingleFileMultisites 0.023s passed

Standard error

19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 7:01:56 PM GMT
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:56.985 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:56.986 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:01:56.986 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:01:56.986 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:01:56.986 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:01:56.986 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:01:56.988 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:01:56.991 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
19:01:56.991 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:01:56.991 INFO  ProgressMeter - Starting traversal
19:01:56.991 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:01:56.995 INFO  ProgressMeter -             unmapped              0.0                     4          60000.0
19:01:56.995 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
19:01:56.995 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 7:01:56 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.011 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:01:57.012 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:01:57.013 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:01:57.016 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:01:57.029 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:01:57.029 INFO  ProgressMeter - Starting traversal
19:01:57.029 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:01:57.031 INFO  ProgressMeter -             unmapped              0.0                    21         630000.0
19:01:57.031 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
19:01:57.031 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.033 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:01:57.034 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:01:57.056 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:01:57.058 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:01:57.060 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
19:01:57.074 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:01:57.075 INFO  ProgressMeter - Starting traversal
19:01:57.075 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:01:57.076 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
19:01:57.076 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
19:01:57.076 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.078 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:01:57.095 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:01:57.097 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:01:57.098 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
19:01:57.112 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:01:57.112 INFO  ProgressMeter - Starting traversal
19:01:57.112 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:01:57.114 INFO  ProgressMeter -             unmapped              0.0                    20         600000.0
19:01:57.114 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
19:01:57.114 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.116 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
19:01:57.134 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
19:01:57.136 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
19:01:57.139 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
19:01:57.139 INFO  ProgressMeter - Starting traversal
19:01:57.139 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:01:57.139 INFO  ProgressMeter -             unmapped              0.0                     7         Infinity
19:01:57.139 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
19:01:57.139 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864