Class org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest

all > org.broadinstitute.hellbender.engine > MultiplePassReadWalkerUnitTest
tests
failures
ignored
0.336s
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)	0.040s	passed
testPassCounts[0](0)	0.023s	passed
testPassCounts[1](1)	0.017s	passed
testPassCounts[2](2)	0.023s	passed
testPassCounts[3](5)	0.022s	passed
testPassCounts[4](25)	0.028s	passed
testRejectAttemptToIndexNonIndexableInput[0](/count_reads.bam)	0.025s	passed
testRejectAttemptToIndexNonIndexableInput[1](/count_reads.sam)	0.025s	passed
testRejectAttemptToIndexNonIndexableInput[2](/count_reads.cram)	0.026s	passed
testTwoPass[0](/count_reads.bam)	0.023s	passed
testTwoPass[1](/count_reads.sam)	0.025s	passed
testTwoPass[2](/count_reads.cram)	0.028s	passed
Standard error

16:12:11.824 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.824 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.825 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.825 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.825 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.825 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.825 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.825 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.825 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.825 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.825 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.825 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.825 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:11.825 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:11.825 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:11.825 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:11.825 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:11.831 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
16:12:11.831 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:11.832 INFO  ProgressMeter - Starting traversal
16:12:11.832 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:11.833 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.834 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:11.834 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.834 INFO  ProgressMeter -             unmapped              0.0                    10         300000.0
16:12:11.834 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
16:12:11.834 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.855 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.855 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.855 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.855 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.855 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.855 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.855 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.855 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.855 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.855 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.855 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.855 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.855 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:11.855 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:11.855 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:11.855 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:11.855 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:11.866 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
16:12:11.866 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:11.866 INFO  ProgressMeter - Starting traversal
16:12:11.866 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:11.872 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.872 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:11.875 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.875 INFO  ProgressMeter -             unmapped              0.0                    10          66666.7
16:12:11.875 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
16:12:11.875 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.897 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.897 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.897 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.897 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.897 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.897 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.897 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.897 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.898 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.898 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.898 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.898 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.898 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:11.898 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:11.898 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:11.898 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:11.898 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:11.899 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:11.899 INFO  ProgressMeter - Starting traversal
16:12:11.899 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:11.899 INFO  ProgressMeter -             unmapped              0.0                     0              NaN
16:12:11.899 INFO  ProgressMeter - Traversal complete. Processed 0 total reads in 0.0 minutes.
16:12:11.899 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.914 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.914 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.914 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.914 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.914 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.915 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.915 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.915 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.915 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.915 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.915 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.915 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.915 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:11.915 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:11.915 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:11.915 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:11.915 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:11.915 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:11.915 INFO  ProgressMeter - Starting traversal
16:12:11.915 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:11.916 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.916 INFO  ProgressMeter -             unmapped              0.0                     8         480000.0
16:12:11.916 INFO  ProgressMeter - Traversal complete. Processed 8 total reads in 0.0 minutes.
16:12:11.916 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.937 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.937 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.937 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.937 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.937 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.937 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.937 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.937 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.937 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.937 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.937 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.937 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.937 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:11.937 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:11.937 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:11.937 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:11.937 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:11.938 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:11.938 INFO  ProgressMeter - Starting traversal
16:12:11.938 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:11.938 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.938 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:11.938 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.939 INFO  ProgressMeter -             unmapped              0.0                    16         960000.0
16:12:11.939 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
16:12:11.939 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.959 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.959 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.959 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.959 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.959 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.959 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.959 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.959 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.959 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.959 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.959 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.959 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.959 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:11.959 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:11.959 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:11.959 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:11.959 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:11.959 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:11.959 INFO  ProgressMeter - Starting traversal
16:12:11.960 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:11.960 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.960 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:11.960 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.960 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
16:12:11.960 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.960 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
16:12:11.961 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.961 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
16:12:11.961 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.961 INFO  ProgressMeter -             unmapped              0.0                    40        2400000.0
16:12:11.961 INFO  ProgressMeter - Traversal complete. Processed 40 total reads in 0.0 minutes.
16:12:11.961 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:11.982 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.982 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:11.982 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:11.982 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:11.982 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:11.982 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:11 PM GMT
16:12:11.982 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.982 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:11.982 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:11.982 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:11.982 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:11.982 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:11.982 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:11.982 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:11.982 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:11.982 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:11.982 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:11.983 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:11.983 INFO  ProgressMeter - Starting traversal
16:12:11.983 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:11.983 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.983 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:11.983 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.983 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
16:12:11.983 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.983 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
16:12:11.984 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.984 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
16:12:11.984 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.984 INFO  dummyMultiplePassReadWalker - Starting traversal pass 6
16:12:11.984 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.984 INFO  dummyMultiplePassReadWalker - Starting traversal pass 7
16:12:11.984 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.984 INFO  dummyMultiplePassReadWalker - Starting traversal pass 8
16:12:11.984 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.984 INFO  dummyMultiplePassReadWalker - Starting traversal pass 9
16:12:11.985 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.985 INFO  dummyMultiplePassReadWalker - Starting traversal pass 10
16:12:11.985 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.985 INFO  dummyMultiplePassReadWalker - Starting traversal pass 11
16:12:11.985 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.985 INFO  dummyMultiplePassReadWalker - Starting traversal pass 12
16:12:11.985 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.985 INFO  dummyMultiplePassReadWalker - Starting traversal pass 13
16:12:11.985 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.985 INFO  dummyMultiplePassReadWalker - Starting traversal pass 14
16:12:11.986 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.986 INFO  dummyMultiplePassReadWalker - Starting traversal pass 15
16:12:11.986 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.986 INFO  dummyMultiplePassReadWalker - Starting traversal pass 16
16:12:11.986 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.986 INFO  dummyMultiplePassReadWalker - Starting traversal pass 17
16:12:11.986 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.986 INFO  dummyMultiplePassReadWalker - Starting traversal pass 18
16:12:11.986 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.986 INFO  dummyMultiplePassReadWalker - Starting traversal pass 19
16:12:11.987 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.987 INFO  dummyMultiplePassReadWalker - Starting traversal pass 20
16:12:11.987 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.987 INFO  dummyMultiplePassReadWalker - Starting traversal pass 21
16:12:11.987 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.987 INFO  dummyMultiplePassReadWalker - Starting traversal pass 22
16:12:11.987 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.987 INFO  dummyMultiplePassReadWalker - Starting traversal pass 23
16:12:11.987 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.987 INFO  dummyMultiplePassReadWalker - Starting traversal pass 24
16:12:11.987 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.987 INFO  dummyMultiplePassReadWalker - Starting traversal pass 25
16:12:11.988 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:11.988 INFO  ProgressMeter -             unmapped              0.0                   200        2400000.0
16:12:11.988 INFO  ProgressMeter - Traversal complete. Processed 200 total reads in 0.0 minutes.
16:12:11.988 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:11 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:12.010 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.010 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:12.010 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:12.010 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:12.010 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:12.010 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:12 PM GMT
16:12:12.010 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.010 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.010 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:12.010 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:12.010 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:12.010 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:12.010 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:12.010 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:12.010 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:12.010 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:12.010 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:12.014 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
16:12:12.015 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:12 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:12.035 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.035 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:12.035 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:12.035 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:12.035 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:12.035 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:12 PM GMT
16:12:12.035 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.035 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.035 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:12.035 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:12.035 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:12.035 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:12.035 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:12.035 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:12.035 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:12.035 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:12.035 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:12.040 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
16:12:12.040 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:12 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:12.061 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.061 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:12.061 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:12.061 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:12.061 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:12.061 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:12 PM GMT
16:12:12.061 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.061 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.061 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:12.061 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:12.061 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:12.061 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:12.061 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:12.061 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:12.061 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:12.061 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:12.061 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:12.065 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
16:12:12.065 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:12 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:12.086 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.086 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:12.086 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:12.086 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:12.086 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:12.086 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:12 PM GMT
16:12:12.086 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.086 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.086 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:12.086 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:12.086 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:12.086 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:12.086 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:12.086 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:12.086 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:12.086 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:12.086 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:12.088 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:12.088 INFO  ProgressMeter - Starting traversal
16:12:12.088 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:12.088 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:12.088 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:12.088 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:12.088 INFO  ProgressMeter -             unmapped              0.0                    16         Infinity
16:12:12.088 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
16:12:12.088 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:12 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:12.108 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.108 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:12.109 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:12.109 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:12.109 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:12.109 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:12 PM GMT
16:12:12.109 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.109 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.109 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:12.109 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:12.109 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:12.109 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:12.109 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:12.109 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:12.109 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:12.109 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:12.109 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:12.110 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:12.110 INFO  ProgressMeter - Starting traversal
16:12:12.110 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:12.113 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:12.114 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:12.114 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:12.114 INFO  ProgressMeter -             unmapped              0.0                    16         240000.0
16:12:12.114 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
16:12:12.114 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:12 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:12.134 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.135 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-g6e00a37-SNAPSHOT
16:12:12.135 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:12.135 INFO  dummyMultiplePassReadWalker - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:12:12.135 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:12.135 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 5, 2025 at 4:12:12 PM GMT
16:12:12.135 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.135 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
16:12:12.135 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:12.135 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:12.135 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:12.135 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:12.135 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
16:12:12.135 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
16:12:12.135 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
16:12:12.135 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
16:12:12.135 INFO  dummyMultiplePassReadWalker - Initializing engine
16:12:12.136 INFO  dummyMultiplePassReadWalker - Done initializing engine
16:12:12.136 INFO  ProgressMeter - Starting traversal
16:12:12.136 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:12:12.140 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:12.140 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
16:12:12.143 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

16:12:12.143 INFO  ProgressMeter -             unmapped              0.0                    16         137142.9
16:12:12.143 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
16:12:12.143 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 5, 2025 at 4:12:12 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000