Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

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

tests
0

failures
0

ignored
0.210s

duration
100%

successful

Tests

Test Duration Result
testIgnoreVariantsThatStartOutsideInterval 0.033s passed
testMergingTwoFilesCorrectBehavior 0.055s passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf) 0.047s 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 0.028s passed

Standard error

16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
16:12:11.612 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
16:12:11.615 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
16:12:11.618 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
16:12:11.619 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
16:12:11.619 INFO  ProgressMeter - Starting traversal
16:12:11.619 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
16:12:11.623 INFO  ProgressMeter -             unmapped              0.0                     4          60000.0
16:12:11.623 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
16:12:11.623 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
16:12:11.645 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
16:12:11.647 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
16:12:11.649 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
16:12:11.667 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
16:12:11.667 INFO  ProgressMeter - Starting traversal
16:12:11.667 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
16:12:11.669 INFO  ProgressMeter -             unmapped              0.0                    21         630000.0
16:12:11.669 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
16:12:11.669 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.670 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
16:12:11.672 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
16:12:11.700 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
16:12:11.702 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
16:12:11.704 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
16:12:11.721 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
16:12:11.721 INFO  ProgressMeter - Starting traversal
16:12:11.721 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
16:12:11.722 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
16:12:11.722 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
16:12:11.722 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.724 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
16:12:11.747 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
16:12:11.749 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
16:12:11.751 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
16:12:11.768 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
16:12:11.768 INFO  ProgressMeter - Starting traversal
16:12:11.768 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
16:12:11.769 INFO  ProgressMeter -             unmapped              0.0                    20        1200000.0
16:12:11.769 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
16:12:11.769 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.771 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
16:12:11.794 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
16:12:11.796 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
16:12:11.798 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
16:12:11.798 INFO  ProgressMeter - Starting traversal
16:12:11.798 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
16:12:11.799 INFO  ProgressMeter -             unmapped              0.0                     7         420000.0
16:12:11.799 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
16:12:11.799 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000