Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

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

tests
0

failures
0

ignored
0.220s

duration
100%

successful

Tests

Test Duration Result
testIgnoreVariantsThatStartOutsideInterval 0.027s passed
testMergingTwoFilesCorrectBehavior 0.072s passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf) 0.048s passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf) 0.046s passed
testSingleFileMultisites 0.027s passed

Standard error

21:17:52.217 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.217 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
21:17:52.218 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
21:17:52.220 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
21:17:52.223 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
21:17:52.224 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
21:17:52.224 INFO  ProgressMeter - Starting traversal
21:17:52.224 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
21:17:52.227 INFO  ProgressMeter -             unmapped              0.0                     4          80000.0
21:17:52.227 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
21:17:52.227 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.244 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.244 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.244 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.244 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
21:17:52.245 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
21:17:52.246 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
21:17:52.249 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
21:17:52.264 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
21:17:52.264 INFO  ProgressMeter - Starting traversal
21:17:52.264 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
21:17:52.276 INFO  ProgressMeter -             unmapped              0.0                    21         105000.0
21:17:52.276 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
21:17:52.276 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.290 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
21:17:52.292 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
21:17:52.322 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
21:17:52.323 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
21:17:52.323 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
21:17:52.324 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
21:17:52.326 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
21:17:52.344 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
21:17:52.344 INFO  ProgressMeter - Starting traversal
21:17:52.344 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
21:17:52.345 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
21:17:52.346 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
21:17:52.346 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.347 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
21:17:52.370 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
21:17:52.372 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
21:17:52.374 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
21:17:52.391 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
21:17:52.391 INFO  ProgressMeter - Starting traversal
21:17:52.391 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
21:17:52.393 INFO  ProgressMeter -             unmapped              0.0                    20         600000.0
21:17:52.393 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
21:17:52.393 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.394 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
21:17:52.417 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.417 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.417 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.417 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.417 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.417 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.417 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
21:17:52.418 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
21:17:52.419 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
21:17:52.422 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
21:17:52.422 INFO  ProgressMeter - Starting traversal
21:17:52.422 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
21:17:52.422 INFO  ProgressMeter -             unmapped              0.0                     7         Infinity
21:17:52.422 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
21:17:52.422 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560