Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

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

tests
0

failures
0

ignored
0.122s

duration
100%

successful

Tests

Test Duration Result
testIgnoreVariantsThatStartOutsideInterval 0.017s passed
testMergingTwoFilesCorrectBehavior 0.035s passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf) 0.030s 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 0.013s passed

Standard error

14:51:05.029 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.029 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:05.029 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:05.029 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:05.029 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 2:51:05 PM UTC
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
14:51:05.030 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
14:51:05.032 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
14:51:05.035 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
14:51:05.035 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
14:51:05.036 INFO  ProgressMeter - Starting traversal
14:51:05.036 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:51:05.039 INFO  ProgressMeter -             unmapped              0.0                     4          80000.0
14:51:05.039 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
14:51:05.039 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 2:51:05 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 2:51:05 PM UTC
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.046 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
14:51:05.047 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
14:51:05.048 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
14:51:05.050 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
14:51:05.064 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
14:51:05.064 INFO  ProgressMeter - Starting traversal
14:51:05.065 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:51:05.066 INFO  ProgressMeter -             unmapped              0.0                    21        1260000.0
14:51:05.066 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
14:51:05.066 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 2:51:05 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:05.068 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
14:51:05.069 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 2:51:05 PM UTC
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
14:51:05.082 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
14:51:05.084 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
14:51:05.086 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
14:51:05.102 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
14:51:05.102 INFO  ProgressMeter - Starting traversal
14:51:05.102 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:51:05.104 INFO  ProgressMeter -             unmapped              0.0                    22         660000.0
14:51:05.104 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
14:51:05.104 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 2:51:05 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:05.106 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 2:51:05 PM UTC
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.112 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
14:51:05.113 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
14:51:05.115 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
14:51:05.116 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
14:51:05.129 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
14:51:05.129 INFO  ProgressMeter - Starting traversal
14:51:05.129 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:51:05.131 INFO  ProgressMeter -             unmapped              0.0                    20         600000.0
14:51:05.131 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
14:51:05.131 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 2:51:05 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
14:51:05.133 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
14:51:05.140 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: March 4, 2026 at 2:51:05 PM UTC
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
14:51:05.141 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
14:51:05.143 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
14:51:05.145 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
14:51:05.145 INFO  ProgressMeter - Starting traversal
14:51:05.145 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:51:05.146 INFO  ProgressMeter -             unmapped              0.0                     7         420000.0
14:51:05.146 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
14:51:05.146 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[March 4, 2026 at 2:51:05 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600