Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerGroupedOnStartUnitTest
tests
failures
ignored
0.134s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIgnoreVariantsThatStartOutsideInterval	0.022s	passed
testMergingTwoFilesCorrectBehavior	0.041s	passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf)	0.029s	passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf)	0.026s	passed
testSingleFileMultisites	0.016s	passed
Standard error

22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.696 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:32:02.697 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:32:02.699 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:32:02.703 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
22:32:02.704 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:32:02.704 INFO  ProgressMeter - Starting traversal
22:32:02.704 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:32:02.708 INFO  ProgressMeter -             unmapped              0.0                     4          60000.0
22:32:02.708 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
22:32:02.708 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:32:02.717 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:32:02.719 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:32:02.721 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:32:02.739 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:32:02.739 INFO  ProgressMeter - Starting traversal
22:32:02.739 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:32:02.741 INFO  ProgressMeter -             unmapped              0.0                    21         630000.0
22:32:02.741 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
22:32:02.741 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.743 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:32:02.744 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.756 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:32:02.757 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:32:02.758 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:32:02.761 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
22:32:02.775 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:32:02.775 INFO  ProgressMeter - Starting traversal
22:32:02.775 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:32:02.777 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
22:32:02.777 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
22:32:02.777 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.778 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.785 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:32:02.786 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:32:02.787 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:32:02.789 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
22:32:02.802 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:32:02.802 INFO  ProgressMeter - Starting traversal
22:32:02.802 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:32:02.803 INFO  ProgressMeter -             unmapped              0.0                    20        1200000.0
22:32:02.803 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
22:32:02.803 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
22:32:02.805 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 28, 2025 at 10:32:02 PM UTC
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
22:32:02.812 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
22:32:02.818 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
22:32:02.820 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
22:32:02.820 INFO  ProgressMeter - Starting traversal
22:32:02.820 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:32:02.821 INFO  ProgressMeter -             unmapped              0.0                     7         420000.0
22:32:02.821 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
22:32:02.821 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 28, 2025 at 10:32:02 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600