Class org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerGroupedOnStartUnitTest
tests
failures
ignored
0.093s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIgnoreVariantsThatStartOutsideInterval	0.016s	passed
testMergingTwoFilesCorrectBehavior	0.028s	passed
testSimpleCaseDuplicateFile[0](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.copy.vcf)	0.021s	passed
testSimpleCaseDuplicateFile[1](src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf, src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.copy.vcf)	0.020s	passed
testSingleFileMultisites	0.008s	passed
Standard error

20:13:38.128 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.128 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:38.128 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:38.128 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:38.128 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:13:38 PM UTC
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:13:38.129 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:13:38.130 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:13:38.133 INFO  IntervalArgumentCollection - Processing 41 bp from intervals
20:13:38.133 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:13:38.133 INFO  ProgressMeter - Starting traversal
20:13:38.134 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:13:38.136 INFO  ProgressMeter -             unmapped              0.0                     4         120000.0
20:13:38.136 INFO  ProgressMeter - Traversal complete. Processed 4 total variants in 0.0 minutes.
20:13:38.136 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:13:38 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:13:38 PM UTC
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:13:38.142 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:13:38.143 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:13:38.145 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:13:38.156 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:13:38.156 INFO  ProgressMeter - Starting traversal
20:13:38.156 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:13:38.158 INFO  ProgressMeter -             unmapped              0.0                    21        1260000.0
20:13:38.158 INFO  ProgressMeter - Traversal complete. Processed 21 total variants in 0.0 minutes.
20:13:38.158 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:13:38 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:38.159 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:13:38.160 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:13:38 PM UTC
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:13:38.170 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:13:38.171 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:13:38.173 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
20:13:38.183 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:13:38.183 INFO  ProgressMeter - Starting traversal
20:13:38.183 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:13:38.184 INFO  ProgressMeter -             unmapped              0.0                    22        1320000.0
20:13:38.184 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
20:13:38.184 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:13:38 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:38.185 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample1.vcf
20:13:38.190 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.190 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:13:38 PM UTC
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:13:38.191 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:13:38.192 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:13:38.193 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
20:13:38.203 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:13:38.203 INFO  ProgressMeter - Starting traversal
20:13:38.203 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:13:38.204 INFO  ProgressMeter -             unmapped              0.0                    20         Infinity
20:13:38.205 INFO  ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
20:13:38.205 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:13:38 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416
20:13:38.205 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample2.vcf
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - Executing as runner@fv-az1120-225 on Linux v6.8.0-1020-azure amd64
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - Start Date/Time: February 10, 2025 at 8:13:38 PM UTC
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - ------------------------------------------------------------
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - Deflater: IntelDeflater
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - Inflater: IntelInflater
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - GCS max retries/reopens: 20
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - Requester pays: disabled
20:13:38.211 INFO  DummyExampleGroupingMultiVariantWalker - Initializing engine
20:13:38.213 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart/gvcfExample3.vcf
20:13:38.214 INFO  DummyExampleGroupingMultiVariantWalker - Done initializing engine
20:13:38.214 INFO  ProgressMeter - Starting traversal
20:13:38.214 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
20:13:38.214 INFO  ProgressMeter -             unmapped              0.0                     7         Infinity
20:13:38.215 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
20:13:38.215 INFO  DummyExampleGroupingMultiVariantWalker - Shutting down engine
[February 10, 2025 at 8:13:38 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStartUnitTest$DummyExampleGroupingMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=750780416