Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

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

tests
0

failures
0

ignored
0.171s

duration
100%

successful

Tests

Test Duration Result
testIgnoreVariantsThatStartOutsideInterval 0.026s passed
testMergingTwoFilesCorrectBehavior 0.042s passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf) 0.042s 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

15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 3:09:17 PM GMT
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
15:09:17.923 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
15:09:17.925 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
15:09:17.928 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
15:09:17.929 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
15:09:17.929 INFO  ProgressMeter - Starting traversal
15:09:17.929 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:17.932 INFO  ProgressMeter -             unmapped              0.0                     4          80000.0
15:09:17.932 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
15:09:17.932 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 3:09:17 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:17.948 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 3:09:17 PM GMT
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
15:09:17.949 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
15:09:17.950 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
15:09:17.952 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
15:09:17.965 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
15:09:17.965 INFO  ProgressMeter - Starting traversal
15:09:17.965 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:17.967 INFO  ProgressMeter -             unmapped              0.0                    21         630000.0
15:09:17.967 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
15:09:17.967 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 3:09:17 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:17.969 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
15:09:17.970 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 3:09:17 PM GMT
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:17.991 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
15:09:17.992 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
15:09:17.992 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
15:09:17.992 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
15:09:17.992 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
15:09:17.994 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
15:09:17.996 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf
15:09:18.011 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
15:09:18.012 INFO  ProgressMeter - Starting traversal
15:09:18.012 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:18.014 INFO  ProgressMeter -             unmapped              0.0                    22         660000.0
15:09:18.014 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
15:09:18.014 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 3:09:18 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:18.016 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 3:09:18 PM GMT
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
15:09:18.034 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
15:09:18.036 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
15:09:18.038 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf
15:09:18.051 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
15:09:18.051 INFO  ProgressMeter - Starting traversal
15:09:18.051 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:18.053 INFO  ProgressMeter -             unmapped              0.0                    20         600000.0
15:09:18.053 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
15:09:18.053 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 3:09:18 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976
15:09:18.055 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - The Genome Analysis Toolkit (GATK) vafter_master_merge-284-g4157897-SNAPSHOT
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 3:09:18 PM GMT
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:09:18.072 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
15:09:18.073 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
15:09:18.073 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
15:09:18.073 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
15:09:18.073 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
15:09:18.075 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
15:09:18.077 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
15:09:18.077 INFO  ProgressMeter - Starting traversal
15:09:18.077 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:09:18.078 INFO  ProgressMeter -             unmapped              0.0                     7         420000.0
15:09:18.078 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
15:09:18.078 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 3:09:18 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=813694976