Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

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

tests
0

failures
0

ignored
0.102s

duration
100%

successful

Tests

Test Duration Result
testIgnoreVariantsThatStartOutsideInterval 0.018s passed
testMergingTwoFilesCorrectBehavior 0.027s passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf) 0.020s passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf) 0.027s passed
testSingleFileMultisites 0.010s passed

Standard error

18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
18:46:04.535 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
18:46:04.539 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
18:46:04.541 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
18:46:04.542 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
18:46:04.542 INFO  ProgressMeter - Starting traversal
18:46:04.542 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:46:04.545 INFO  ProgressMeter -             unmapped              0.0                     4          80000.0
18:46:04.545 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
18:46:04.545 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.550 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
18:46:04.551 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
18:46:04.552 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
18:46:04.553 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
18:46:04.563 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
18:46:04.563 INFO  ProgressMeter - Starting traversal
18:46:04.563 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:46:04.564 INFO  ProgressMeter -             unmapped              0.0                    21        1260000.0
18:46:04.565 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
18:46:04.565 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.566 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
18:46:04.567 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
18:46:04.578 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
18:46:04.579 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
18:46:04.581 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
18:46:04.590 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
18:46:04.590 INFO  ProgressMeter - Starting traversal
18:46:04.590 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:46:04.591 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
18:46:04.592 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
18:46:04.592 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.593 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
18:46:04.598 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.598 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.598 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.598 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.598 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.598 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.598 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
18:46:04.599 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
18:46:04.600 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
18:46:04.607 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
18:46:04.617 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
18:46:04.617 INFO  ProgressMeter - Starting traversal
18:46:04.617 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:46:04.618 INFO  ProgressMeter -             unmapped              0.0                    20        1200000.0
18:46:04.618 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
18:46:04.618 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.619 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.625 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
18:46:04.626 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
18:46:04.627 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
18:46:04.629 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
18:46:04.629 INFO  ProgressMeter - Starting traversal
18:46:04.629 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
18:46:04.629 INFO  ProgressMeter -             unmapped              0.0                     7         Infinity
18:46:04.629 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
18:46:04.629 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600