Class org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest

all > org.broadinstitute.hellbender.engine > LocusWalkerByIntervalUnitTest
13

tests
0

failures
0

ignored
0.304s

duration
100%

successful

Tests

Test Duration Result
testOverlappingBasesCoverageInformation[0]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@6cce1f60, [I@1ca3d997) 0.033s passed
testOverlappingBasesCoverageInformation[10]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@61e67cc1, [I@118bace5) 0.019s passed
testOverlappingBasesCoverageInformation[11]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@2c890ee3, [I@62068fa5) 0.027s passed
testOverlappingBasesCoverageInformation[12]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@414c63f1, [I@e6522bd) 0.028s passed
testOverlappingBasesCoverageInformation[1]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@160423e0, [I@3fc8a6c0) 0.020s passed
testOverlappingBasesCoverageInformation[2]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@737fd68, [I@7e1b750e) 0.020s passed
testOverlappingBasesCoverageInformation[3]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@39d06cd9, [I@6c82ecbe) 0.027s passed
testOverlappingBasesCoverageInformation[4]([20:1000-2000, 20:2001-3000], [Lhtsjdk.samtools.util.Locatable;@14270715, [I@3b829ef) 0.021s passed
testOverlappingBasesCoverageInformation[5]([20:1000-2000, 20:3001-4000], [Lhtsjdk.samtools.util.Locatable;@2ff35d7, [I@54856056) 0.022s passed
testOverlappingBasesCoverageInformation[6]([20:1000-2000, 21:3001-4000], [Lhtsjdk.samtools.util.Locatable;@6911005b, [I@6b7d363c) 0.026s passed
testOverlappingBasesCoverageInformation[7]([20:1000-2000, 20:3001-4000], [Lhtsjdk.samtools.util.Locatable;@42becaf6, [I@51934be2) 0.026s passed
testOverlappingBasesCoverageInformation[8]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@5d33426a, [I@7b8b458e) 0.018s passed
testOverlappingBasesCoverageInformation[9]([20:1000-2000], [Lhtsjdk.samtools.util.Locatable;@58f0d3b6, [I@e124366) 0.017s passed

Standard error

20:25:21.445 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.445 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.445 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.445 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.445 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.445 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.445 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.445 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.446 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.446 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.446 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.446 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.446 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.446 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.446 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.446 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.446 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.448 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.448 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.448 INFO  ProgressMeter - Starting traversal
20:25:21.448 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.462 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.462 INFO  ProgressMeter -              20:1999              0.0                  1001        4290000.0
20:25:21.463 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.463 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.478 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.478 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.478 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.478 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.478 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.478 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.478 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.478 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.478 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.479 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.479 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.479 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.479 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.479 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.479 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.479 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.479 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.480 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.480 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.480 INFO  ProgressMeter - Starting traversal
20:25:21.480 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.482 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.482 INFO  ProgressMeter -              20:1999              0.0                  1001       60060000.0
20:25:21.483 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.483 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.498 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.498 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.498 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.498 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.498 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.498 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.498 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.498 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.498 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.498 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.498 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.498 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.498 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.498 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.499 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.499 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.499 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.500 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.501 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.501 INFO  ProgressMeter - Starting traversal
20:25:21.501 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.503 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.503 INFO  ProgressMeter -              20:1999              0.0                  1001       30030000.0
20:25:21.503 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.503 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.525 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.525 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.525 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.525 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.525 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.526 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.526 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.526 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.526 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.526 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.526 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.526 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.526 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.526 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.526 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.526 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.526 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.528 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.528 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.528 INFO  ProgressMeter - Starting traversal
20:25:21.528 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.531 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.531 INFO  ProgressMeter -              20:1999              0.0                  1001       20020000.0
20:25:21.531 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.531 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.546 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.547 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.547 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.547 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.547 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.547 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.547 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.547 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.547 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.547 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.547 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.547 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.547 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.547 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.547 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.547 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.547 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.549 INFO  IntervalArgumentCollection - Processing 2001 bp from intervals
20:25:21.549 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.549 INFO  ProgressMeter - Starting traversal
20:25:21.549 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.552 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.552 INFO  ProgressMeter -              20:2999              0.0                  2001       40020000.0
20:25:21.552 INFO  ProgressMeter - Traversal complete. Processed 2001 total loci in 0.0 minutes.
20:25:21.552 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.568 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.568 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.568 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.568 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.568 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.568 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.568 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.568 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.568 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.568 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.569 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.569 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.569 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.569 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.569 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.569 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.569 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.571 INFO  IntervalArgumentCollection - Processing 2001 bp from intervals
20:25:21.571 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.571 INFO  ProgressMeter - Starting traversal
20:25:21.571 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.574 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.574 INFO  ProgressMeter -              20:3999              0.0                  2001       40020000.0
20:25:21.574 INFO  ProgressMeter - Traversal complete. Processed 2001 total loci in 0.0 minutes.
20:25:21.574 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.595 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.595 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.595 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.595 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.595 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.595 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.595 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.595 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.595 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.595 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.596 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.596 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.596 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.596 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.596 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.596 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.596 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.597 INFO  IntervalArgumentCollection - Processing 2001 bp from intervals
20:25:21.597 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.597 INFO  ProgressMeter - Starting traversal
20:25:21.597 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.600 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.600 INFO  ProgressMeter -              21:3999              0.0                  2001       60030000.0
20:25:21.601 INFO  ProgressMeter - Traversal complete. Processed 2001 total loci in 0.0 minutes.
20:25:21.601 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.616 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.616 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.616 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.616 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.616 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.616 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.616 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.617 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.617 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.617 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.617 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.617 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.617 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.617 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.617 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.617 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.617 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.618 INFO  IntervalArgumentCollection - Processing 2001 bp from intervals
20:25:21.618 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.618 INFO  ProgressMeter - Starting traversal
20:25:21.619 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.626 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.626 INFO  ProgressMeter -              20:3999              0.0                  2001       17151428.6
20:25:21.626 INFO  ProgressMeter - Traversal complete. Processed 2001 total loci in 0.0 minutes.
20:25:21.626 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.641 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.641 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.642 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.642 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.642 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.642 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.642 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.642 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.642 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.642 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.642 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.642 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.642 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.642 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.642 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.642 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.642 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.643 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.644 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.644 INFO  ProgressMeter - Starting traversal
20:25:21.644 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.645 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.645 INFO  ProgressMeter -              20:1999              0.0                  1001       60060000.0
20:25:21.645 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.645 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.660 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.660 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.660 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.660 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.660 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.660 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.660 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.660 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.660 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.660 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.660 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.660 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.660 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.660 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.660 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.660 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.660 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.661 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.661 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.661 INFO  ProgressMeter - Starting traversal
20:25:21.662 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.663 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.663 INFO  ProgressMeter -              20:1999              0.0                  1001       60060000.0
20:25:21.663 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.663 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.678 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.678 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.678 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.678 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.678 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.678 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.678 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.678 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.678 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.678 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.678 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.678 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.678 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.678 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.678 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.678 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.678 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.680 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.680 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.680 INFO  ProgressMeter - Starting traversal
20:25:21.680 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.683 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.683 INFO  ProgressMeter -              20:1999              0.0                  1001       20020000.0
20:25:21.683 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.683 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.704 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.705 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.705 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.705 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.705 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.705 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.705 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.705 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.705 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.705 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.705 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.705 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.705 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.705 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.705 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.705 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.705 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.707 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.707 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.707 INFO  ProgressMeter - Starting traversal
20:25:21.707 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.709 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.709 INFO  ProgressMeter -              20:1999              0.0                  1001       60060000.0
20:25:21.710 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.710 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:21.732 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.732 INFO  TestTransformedLocusWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:21.732 INFO  TestTransformedLocusWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:21.732 INFO  TestTransformedLocusWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:21.732 INFO  TestTransformedLocusWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:21.732 INFO  TestTransformedLocusWalker - Start Date/Time: February 10, 2025 at 8:25:21 PM GMT
20:25:21.732 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.732 INFO  TestTransformedLocusWalker - ------------------------------------------------------------
20:25:21.732 INFO  TestTransformedLocusWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:21.733 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:21.733 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:21.733 INFO  TestTransformedLocusWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:21.733 INFO  TestTransformedLocusWalker - Deflater: IntelDeflater
20:25:21.733 INFO  TestTransformedLocusWalker - Inflater: IntelInflater
20:25:21.733 INFO  TestTransformedLocusWalker - GCS max retries/reopens: 20
20:25:21.733 INFO  TestTransformedLocusWalker - Requester pays: disabled
20:25:21.733 INFO  TestTransformedLocusWalker - Initializing engine
20:25:21.735 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:25:21.735 INFO  TestTransformedLocusWalker - Done initializing engine
20:25:21.735 INFO  ProgressMeter - Starting traversal
20:25:21.735 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:25:21.737 INFO  TestTransformedLocusWalker - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 total reads filtered out of 0 reads processed
20:25:21.737 INFO  ProgressMeter -              20:1999              0.0                  1001       30030000.0
20:25:21.737 INFO  ProgressMeter - Traversal complete. Processed 1001 total loci in 0.0 minutes.
20:25:21.737 INFO  TestTransformedLocusWalker - Shutting down engine
[February 10, 2025 at 8:25:21 PM GMT] org.broadinstitute.hellbender.engine.LocusWalkerByIntervalUnitTest$TestTransformedLocusWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408