Class org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest

all > org.broadinstitute.hellbender.engine > MultiplePassReadWalkerUnitTest
tests
failures
ignored
0.323s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIntervalFiltering[0](/count_reads_sorted.bam)	0.028s	passed
testIntervalFiltering[1](/count_reads_sorted.cram)	0.031s	passed
testPassCounts[0](0)	0.017s	passed
testPassCounts[1](1)	0.017s	passed
testPassCounts[2](2)	0.016s	passed
testPassCounts[3](5)	0.023s	passed
testPassCounts[4](25)	0.028s	passed
testRejectAttemptToIndexNonIndexableInput[0](/count_reads.bam)	0.032s	passed
testRejectAttemptToIndexNonIndexableInput[1](/count_reads.sam)	0.026s	passed
testRejectAttemptToIndexNonIndexableInput[2](/count_reads.cram)	0.026s	passed
testTwoPass[0](/count_reads.bam)	0.025s	passed
testTwoPass[1](/count_reads.sam)	0.026s	passed
testTwoPass[2](/count_reads.cram)	0.028s	passed
Standard error

20:47:50.080 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.081 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.081 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.081 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.081 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.081 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.081 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.081 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.081 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.081 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.081 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.081 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.081 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.081 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.081 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.081 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.081 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.086 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:47:50.087 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.087 INFO  ProgressMeter - Starting traversal
20:47:50.087 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.088 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.089 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.089 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.089 INFO  ProgressMeter -             unmapped              0.0                    10         300000.0
20:47:50.089 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
20:47:50.089 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.105 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.105 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.105 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.105 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.105 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.105 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.105 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.105 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.105 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.105 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.105 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.105 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.105 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.105 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.105 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.105 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.105 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.109 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:47:50.109 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.109 INFO  ProgressMeter - Starting traversal
20:47:50.110 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.119 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.119 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.120 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.120 INFO  ProgressMeter -             unmapped              0.0                    10          60000.0
20:47:50.121 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
20:47:50.121 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.137 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.137 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.137 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.137 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.137 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.137 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.137 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.137 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.137 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.137 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.137 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.137 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.137 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.137 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.137 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.137 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.137 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.138 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.138 INFO  ProgressMeter - Starting traversal
20:47:50.138 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.138 INFO  ProgressMeter -             unmapped              0.0                     0              NaN
20:47:50.138 INFO  ProgressMeter - Traversal complete. Processed 0 total reads in 0.0 minutes.
20:47:50.138 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.153 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.153 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.153 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.153 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.153 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.153 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.153 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.153 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.153 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.153 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.153 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.153 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.153 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.153 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.153 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.153 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.153 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.154 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.154 INFO  ProgressMeter - Starting traversal
20:47:50.154 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.155 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.155 INFO  ProgressMeter -             unmapped              0.0                     8         480000.0
20:47:50.156 INFO  ProgressMeter - Traversal complete. Processed 8 total reads in 0.0 minutes.
20:47:50.156 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.170 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.170 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.170 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.171 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.171 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.171 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.171 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.171 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.171 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.171 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.171 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.171 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.171 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.171 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.172 INFO  ProgressMeter - Starting traversal
20:47:50.172 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.172 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.172 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.172 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.172 INFO  ProgressMeter -             unmapped              0.0                    16         Infinity
20:47:50.172 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:47:50.172 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.193 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.193 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.193 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.193 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.193 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.193 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.193 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.193 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.193 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.193 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.193 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.193 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.193 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.193 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.193 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.193 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.193 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.194 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.194 INFO  ProgressMeter - Starting traversal
20:47:50.194 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.194 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.194 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.195 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.195 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
20:47:50.195 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.195 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
20:47:50.196 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.196 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
20:47:50.196 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.196 INFO  ProgressMeter -             unmapped              0.0                    40        1200000.0
20:47:50.196 INFO  ProgressMeter - Traversal complete. Processed 40 total reads in 0.0 minutes.
20:47:50.196 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.217 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.217 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.217 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.217 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.217 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.217 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.217 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.217 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.217 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.217 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.217 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.217 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.217 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.217 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.217 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.217 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.217 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.217 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.218 INFO  ProgressMeter - Starting traversal
20:47:50.218 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.218 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.218 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.218 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.218 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
20:47:50.218 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.218 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
20:47:50.219 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.219 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
20:47:50.219 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.219 INFO  dummyMultiplePassReadWalker - Starting traversal pass 6
20:47:50.219 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.219 INFO  dummyMultiplePassReadWalker - Starting traversal pass 7
20:47:50.219 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.219 INFO  dummyMultiplePassReadWalker - Starting traversal pass 8
20:47:50.219 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.220 INFO  dummyMultiplePassReadWalker - Starting traversal pass 9
20:47:50.220 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.220 INFO  dummyMultiplePassReadWalker - Starting traversal pass 10
20:47:50.220 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.220 INFO  dummyMultiplePassReadWalker - Starting traversal pass 11
20:47:50.220 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.220 INFO  dummyMultiplePassReadWalker - Starting traversal pass 12
20:47:50.220 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.220 INFO  dummyMultiplePassReadWalker - Starting traversal pass 13
20:47:50.221 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.221 INFO  dummyMultiplePassReadWalker - Starting traversal pass 14
20:47:50.221 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.221 INFO  dummyMultiplePassReadWalker - Starting traversal pass 15
20:47:50.221 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.221 INFO  dummyMultiplePassReadWalker - Starting traversal pass 16
20:47:50.221 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.221 INFO  dummyMultiplePassReadWalker - Starting traversal pass 17
20:47:50.221 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.221 INFO  dummyMultiplePassReadWalker - Starting traversal pass 18
20:47:50.222 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.222 INFO  dummyMultiplePassReadWalker - Starting traversal pass 19
20:47:50.222 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.222 INFO  dummyMultiplePassReadWalker - Starting traversal pass 20
20:47:50.222 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.222 INFO  dummyMultiplePassReadWalker - Starting traversal pass 21
20:47:50.222 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.222 INFO  dummyMultiplePassReadWalker - Starting traversal pass 22
20:47:50.223 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.223 INFO  dummyMultiplePassReadWalker - Starting traversal pass 23
20:47:50.223 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.223 INFO  dummyMultiplePassReadWalker - Starting traversal pass 24
20:47:50.223 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.223 INFO  dummyMultiplePassReadWalker - Starting traversal pass 25
20:47:50.223 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.223 INFO  ProgressMeter -             unmapped              0.0                   200        2400000.0
20:47:50.223 INFO  ProgressMeter - Traversal complete. Processed 200 total reads in 0.0 minutes.
20:47:50.223 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.251 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.251 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.251 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.251 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.251 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.251 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.251 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.251 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.251 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.251 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.251 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.251 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.251 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.251 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.251 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.251 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.251 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.255 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:47:50.256 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.277 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.278 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.278 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.278 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.278 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.278 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.278 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.278 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.278 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.278 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.278 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.278 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.278 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.278 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.278 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.278 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.278 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.283 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:47:50.283 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.304 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.304 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.304 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.304 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.304 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.304 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.304 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.304 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.304 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.304 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.304 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.304 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.304 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.304 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.304 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.304 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.304 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.308 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:47:50.309 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.330 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.330 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.330 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.331 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.331 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.331 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.331 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.331 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.331 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.331 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.331 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.331 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.331 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.331 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.331 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.331 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.331 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.333 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.333 INFO  ProgressMeter - Starting traversal
20:47:50.333 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.333 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.333 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.333 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.333 INFO  ProgressMeter -             unmapped              0.0                    16         Infinity
20:47:50.333 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:47:50.333 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.354 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.354 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.354 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.354 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.354 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.354 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.354 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.354 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.354 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.354 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.354 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.354 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.355 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.355 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.355 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.355 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.355 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.356 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.356 INFO  ProgressMeter - Starting traversal
20:47:50.356 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.359 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.360 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.360 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.360 INFO  ProgressMeter -             unmapped              0.0                    16         240000.0
20:47:50.360 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:47:50.360 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
20:47:50.381 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.381 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-13-g9eb1b78-SNAPSHOT
20:47:50.381 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:50.381 INFO  dummyMultiplePassReadWalker - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:50.381 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:50.381 INFO  dummyMultiplePassReadWalker - Start Date/Time: July 15, 2025 at 8:47:50 PM GMT
20:47:50.381 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.381 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:47:50.381 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:50.381 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:50.381 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:50.381 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:50.381 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:47:50.381 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:47:50.381 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:47:50.381 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:47:50.381 INFO  dummyMultiplePassReadWalker - Initializing engine
20:47:50.383 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:47:50.383 INFO  ProgressMeter - Starting traversal
20:47:50.383 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:47:50.386 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.386 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:47:50.389 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:47:50.389 INFO  ProgressMeter -             unmapped              0.0                    16         160000.0
20:47:50.389 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:47:50.389 INFO  dummyMultiplePassReadWalker - Shutting down engine
[July 15, 2025 at 8:47:50 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912