Class org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest

all > org.broadinstitute.hellbender.engine > MultiplePassReadWalkerUnitTest
tests
failures
ignored
0.303s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIntervalFiltering[0](/count_reads_sorted.bam)	0.031s	passed
testIntervalFiltering[1](/count_reads_sorted.cram)	0.034s	passed
testPassCounts[0](0)	0.018s	passed
testPassCounts[1](1)	0.017s	passed
testPassCounts[2](2)	0.017s	passed
testPassCounts[3](5)	0.018s	passed
testPassCounts[4](25)	0.026s	passed
testRejectAttemptToIndexNonIndexableInput[0](/count_reads.bam)	0.022s	passed
testRejectAttemptToIndexNonIndexableInput[1](/count_reads.sam)	0.021s	passed
testRejectAttemptToIndexNonIndexableInput[2](/count_reads.cram)	0.030s	passed
testTwoPass[0](/count_reads.bam)	0.019s	passed
testTwoPass[1](/count_reads.sam)	0.024s	passed
testTwoPass[2](/count_reads.cram)	0.026s	passed
Standard error

21:17:52.446 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.447 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.447 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.447 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.447 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.447 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.447 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.447 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.447 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.447 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.447 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.447 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.447 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.447 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.447 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.447 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.447 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.453 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
21:17:52.453 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.453 INFO  ProgressMeter - Starting traversal
21:17:52.453 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.455 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.455 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.456 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.456 INFO  ProgressMeter -             unmapped              0.0                    10         200000.0
21:17:52.456 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
21:17:52.456 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.478 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.478 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.478 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.478 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.478 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.478 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.478 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.478 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.478 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.478 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.478 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.478 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.478 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.478 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.478 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.478 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.478 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.483 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
21:17:52.483 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.483 INFO  ProgressMeter - Starting traversal
21:17:52.483 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.488 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.488 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.489 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.489 INFO  ProgressMeter -             unmapped              0.0                    10         100000.0
21:17:52.489 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
21:17:52.489 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.506 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.506 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.506 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.506 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.506 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.506 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.506 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.506 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.506 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.506 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.506 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.506 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.506 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.506 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.506 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.506 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.506 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.507 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.507 INFO  ProgressMeter - Starting traversal
21:17:52.507 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.507 INFO  ProgressMeter -             unmapped              0.0                     0              NaN
21:17:52.507 INFO  ProgressMeter - Traversal complete. Processed 0 total reads in 0.0 minutes.
21:17:52.507 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.523 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.523 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.523 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.523 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.523 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.523 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.523 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.523 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.524 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.524 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.524 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.524 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.524 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.524 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.524 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.524 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.524 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.524 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.524 INFO  ProgressMeter - Starting traversal
21:17:52.524 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.525 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.525 INFO  ProgressMeter -             unmapped              0.0                     8         480000.0
21:17:52.525 INFO  ProgressMeter - Traversal complete. Processed 8 total reads in 0.0 minutes.
21:17:52.525 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.540 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.540 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.540 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.540 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.540 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.540 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.540 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.540 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.540 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.540 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.540 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.540 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.540 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.540 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.540 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.540 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.540 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.541 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.541 INFO  ProgressMeter - Starting traversal
21:17:52.541 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.542 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.542 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.542 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.542 INFO  ProgressMeter -             unmapped              0.0                    16         960000.0
21:17:52.542 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
21:17:52.542 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.558 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.558 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.558 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.558 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.558 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.558 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.558 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.558 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.558 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.558 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.558 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.558 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.558 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.558 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.558 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.558 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.558 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.559 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.559 INFO  ProgressMeter - Starting traversal
21:17:52.559 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.559 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.559 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.560 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.560 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
21:17:52.560 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.560 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
21:17:52.560 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.561 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
21:17:52.561 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.561 INFO  ProgressMeter -             unmapped              0.0                    40        1200000.0
21:17:52.561 INFO  ProgressMeter - Traversal complete. Processed 40 total reads in 0.0 minutes.
21:17:52.561 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.578 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.578 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.578 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.578 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.578 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.579 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.579 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.579 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.579 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.579 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.579 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.579 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.579 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.579 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.579 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.579 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.579 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.579 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.579 INFO  ProgressMeter - Starting traversal
21:17:52.579 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.580 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.580 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.580 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.580 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
21:17:52.580 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.580 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
21:17:52.581 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.581 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
21:17:52.582 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.582 INFO  dummyMultiplePassReadWalker - Starting traversal pass 6
21:17:52.582 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.582 INFO  dummyMultiplePassReadWalker - Starting traversal pass 7
21:17:52.582 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.582 INFO  dummyMultiplePassReadWalker - Starting traversal pass 8
21:17:52.583 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.583 INFO  dummyMultiplePassReadWalker - Starting traversal pass 9
21:17:52.583 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.583 INFO  dummyMultiplePassReadWalker - Starting traversal pass 10
21:17:52.583 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.583 INFO  dummyMultiplePassReadWalker - Starting traversal pass 11
21:17:52.583 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.583 INFO  dummyMultiplePassReadWalker - Starting traversal pass 12
21:17:52.584 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.584 INFO  dummyMultiplePassReadWalker - Starting traversal pass 13
21:17:52.584 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.584 INFO  dummyMultiplePassReadWalker - Starting traversal pass 14
21:17:52.584 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.584 INFO  dummyMultiplePassReadWalker - Starting traversal pass 15
21:17:52.584 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.584 INFO  dummyMultiplePassReadWalker - Starting traversal pass 16
21:17:52.584 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.584 INFO  dummyMultiplePassReadWalker - Starting traversal pass 17
21:17:52.585 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.585 INFO  dummyMultiplePassReadWalker - Starting traversal pass 18
21:17:52.585 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.585 INFO  dummyMultiplePassReadWalker - Starting traversal pass 19
21:17:52.585 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.585 INFO  dummyMultiplePassReadWalker - Starting traversal pass 20
21:17:52.585 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.585 INFO  dummyMultiplePassReadWalker - Starting traversal pass 21
21:17:52.586 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.586 INFO  dummyMultiplePassReadWalker - Starting traversal pass 22
21:17:52.586 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.586 INFO  dummyMultiplePassReadWalker - Starting traversal pass 23
21:17:52.586 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.586 INFO  dummyMultiplePassReadWalker - Starting traversal pass 24
21:17:52.586 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.586 INFO  dummyMultiplePassReadWalker - Starting traversal pass 25
21:17:52.586 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.586 INFO  ProgressMeter -             unmapped              0.0                   200        1714285.7
21:17:52.586 INFO  ProgressMeter - Traversal complete. Processed 200 total reads in 0.0 minutes.
21:17:52.586 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.603 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.603 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.603 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.603 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.603 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.603 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.603 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.603 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.603 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.603 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.603 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.603 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.603 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.603 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.603 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.603 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.603 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.608 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
21:17:52.609 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.625 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.625 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.625 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.625 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.625 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.625 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.625 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.625 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.625 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.625 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.625 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.625 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.625 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.625 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.625 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.625 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.625 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.630 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
21:17:52.630 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.653 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.653 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.653 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.653 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.653 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.653 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.653 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.653 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.653 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.653 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.653 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.653 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.653 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.653 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.653 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.653 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.653 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.659 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
21:17:52.659 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.676 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.676 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.676 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.676 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.676 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.676 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.677 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.677 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.677 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.677 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.677 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.677 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.677 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.677 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.677 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.677 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.677 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.678 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.679 INFO  ProgressMeter - Starting traversal
21:17:52.679 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.679 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.679 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.679 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.679 INFO  ProgressMeter -             unmapped              0.0                    16         Infinity
21:17:52.679 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
21:17:52.679 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.697 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.697 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.697 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.697 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.697 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.697 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.697 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.697 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.698 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.698 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.698 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.698 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.698 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.698 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.698 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.698 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.698 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.699 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.699 INFO  ProgressMeter - Starting traversal
21:17:52.700 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.702 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.703 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.704 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.704 INFO  ProgressMeter -             unmapped              0.0                    16         240000.0
21:17:52.704 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
21:17:52.704 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560
21:17:52.721 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.721 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:52.721 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:52.721 INFO  dummyMultiplePassReadWalker - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:52.721 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:52.721 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 9:17:52 PM GMT
21:17:52.721 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.721 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
21:17:52.721 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:52.721 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:52.721 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:52.721 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:52.721 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
21:17:52.721 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
21:17:52.721 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
21:17:52.721 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
21:17:52.721 INFO  dummyMultiplePassReadWalker - Initializing engine
21:17:52.723 INFO  dummyMultiplePassReadWalker - Done initializing engine
21:17:52.723 INFO  ProgressMeter - Starting traversal
21:17:52.723 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:17:52.727 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.727 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
21:17:52.729 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

21:17:52.729 INFO  ProgressMeter -             unmapped              0.0                    16         160000.0
21:17:52.729 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
21:17:52.729 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 9:17:52 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=849346560