Class org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest

all > org.broadinstitute.hellbender.engine > MultiplePassReadWalkerUnitTest
tests
failures
ignored
0.281s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIntervalFiltering[0](/count_reads_sorted.bam)	0.025s	passed
testIntervalFiltering[1](/count_reads_sorted.cram)	0.029s	passed
testPassCounts[0](0)	0.018s	passed
testPassCounts[1](1)	0.017s	passed
testPassCounts[2](2)	0.017s	passed
testPassCounts[3](5)	0.024s	passed
testPassCounts[4](25)	0.023s	passed
testRejectAttemptToIndexNonIndexableInput[0](/count_reads.bam)	0.022s	passed
testRejectAttemptToIndexNonIndexableInput[1](/count_reads.sam)	0.021s	passed
testRejectAttemptToIndexNonIndexableInput[2](/count_reads.cram)	0.022s	passed
testTwoPass[0](/count_reads.bam)	0.018s	passed
testTwoPass[1](/count_reads.sam)	0.022s	passed
testTwoPass[2](/count_reads.cram)	0.023s	passed
Standard error

19:01:57.158 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.158 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.158 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.158 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.158 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.158 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.158 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.158 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.158 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.158 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.158 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.158 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.158 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.158 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.158 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.158 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.158 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.164 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
19:01:57.164 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.164 INFO  ProgressMeter - Starting traversal
19:01:57.164 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.165 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.166 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.166 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.166 INFO  ProgressMeter -             unmapped              0.0                    10         300000.0
19:01:57.166 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
19:01:57.166 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.182 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.182 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.182 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.183 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.183 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.183 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.183 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.183 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.183 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.183 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.183 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.183 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.183 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.183 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.183 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.183 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.183 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.188 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
19:01:57.189 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.189 INFO  ProgressMeter - Starting traversal
19:01:57.189 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.194 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.194 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.196 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.196 INFO  ProgressMeter -             unmapped              0.0                    10          85714.3
19:01:57.196 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
19:01:57.196 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.213 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.213 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.213 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.214 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.214 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.214 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.214 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.214 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.214 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.214 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.214 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.214 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.214 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.214 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.214 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.214 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.214 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.215 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.215 INFO  ProgressMeter - Starting traversal
19:01:57.215 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.215 INFO  ProgressMeter -             unmapped              0.0                     0              NaN
19:01:57.215 INFO  ProgressMeter - Traversal complete. Processed 0 total reads in 0.0 minutes.
19:01:57.215 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.231 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.231 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.231 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.231 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.231 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.231 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.231 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.231 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.231 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.231 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.231 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.231 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.231 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.231 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.231 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.231 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.231 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.232 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.232 INFO  ProgressMeter - Starting traversal
19:01:57.232 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.233 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.233 INFO  ProgressMeter -             unmapped              0.0                     8         480000.0
19:01:57.233 INFO  ProgressMeter - Traversal complete. Processed 8 total reads in 0.0 minutes.
19:01:57.233 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.248 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.248 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.248 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.248 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.248 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.248 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.248 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.248 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.248 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.248 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.248 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.248 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.248 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.248 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.248 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.248 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.249 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.249 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.249 INFO  ProgressMeter - Starting traversal
19:01:57.249 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.250 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.250 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.250 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.250 INFO  ProgressMeter -             unmapped              0.0                    16         960000.0
19:01:57.250 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
19:01:57.250 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.272 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.272 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.272 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.272 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.272 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.272 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.272 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.272 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.272 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.272 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.272 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.272 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.272 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.272 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.272 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.272 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.272 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.273 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.273 INFO  ProgressMeter - Starting traversal
19:01:57.273 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.273 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.273 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.273 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.274 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
19:01:57.274 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.274 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
19:01:57.274 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.274 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
19:01:57.274 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.274 INFO  ProgressMeter -             unmapped              0.0                    40        2400000.0
19:01:57.274 INFO  ProgressMeter - Traversal complete. Processed 40 total reads in 0.0 minutes.
19:01:57.274 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.290 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.290 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.290 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.290 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.290 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.290 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.290 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.290 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.290 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.290 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.290 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.290 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.290 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.290 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.290 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.290 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.290 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.291 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.291 INFO  ProgressMeter - Starting traversal
19:01:57.291 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.291 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.291 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.292 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.292 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
19:01:57.292 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.292 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
19:01:57.292 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.292 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
19:01:57.292 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.292 INFO  dummyMultiplePassReadWalker - Starting traversal pass 6
19:01:57.293 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.293 INFO  dummyMultiplePassReadWalker - Starting traversal pass 7
19:01:57.293 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.293 INFO  dummyMultiplePassReadWalker - Starting traversal pass 8
19:01:57.293 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.293 INFO  dummyMultiplePassReadWalker - Starting traversal pass 9
19:01:57.293 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.293 INFO  dummyMultiplePassReadWalker - Starting traversal pass 10
19:01:57.293 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.293 INFO  dummyMultiplePassReadWalker - Starting traversal pass 11
19:01:57.294 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.294 INFO  dummyMultiplePassReadWalker - Starting traversal pass 12
19:01:57.294 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.294 INFO  dummyMultiplePassReadWalker - Starting traversal pass 13
19:01:57.294 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.294 INFO  dummyMultiplePassReadWalker - Starting traversal pass 14
19:01:57.294 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.294 INFO  dummyMultiplePassReadWalker - Starting traversal pass 15
19:01:57.295 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.295 INFO  dummyMultiplePassReadWalker - Starting traversal pass 16
19:01:57.295 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.295 INFO  dummyMultiplePassReadWalker - Starting traversal pass 17
19:01:57.295 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.295 INFO  dummyMultiplePassReadWalker - Starting traversal pass 18
19:01:57.295 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.295 INFO  dummyMultiplePassReadWalker - Starting traversal pass 19
19:01:57.296 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.296 INFO  dummyMultiplePassReadWalker - Starting traversal pass 20
19:01:57.296 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.296 INFO  dummyMultiplePassReadWalker - Starting traversal pass 21
19:01:57.296 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.296 INFO  dummyMultiplePassReadWalker - Starting traversal pass 22
19:01:57.296 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.296 INFO  dummyMultiplePassReadWalker - Starting traversal pass 23
19:01:57.297 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.297 INFO  dummyMultiplePassReadWalker - Starting traversal pass 24
19:01:57.297 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.297 INFO  dummyMultiplePassReadWalker - Starting traversal pass 25
19:01:57.297 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.297 INFO  ProgressMeter -             unmapped              0.0                   200        2000000.0
19:01:57.297 INFO  ProgressMeter - Traversal complete. Processed 200 total reads in 0.0 minutes.
19:01:57.297 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.314 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.314 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.314 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.314 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.314 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.314 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.314 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.314 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.314 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.314 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.314 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.314 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.314 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.318 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
19:01:57.319 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.336 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.336 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.336 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.336 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.336 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.336 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.336 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.336 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.336 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.336 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.336 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.336 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.336 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.336 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.336 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.336 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.336 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.340 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
19:01:57.340 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.357 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.357 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.357 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.357 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.357 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.357 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.357 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.357 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.357 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.357 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.357 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.357 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.357 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.357 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.357 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.357 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.357 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.362 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
19:01:57.362 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.379 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.379 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.379 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.379 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.379 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.379 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.379 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.379 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.379 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.379 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.379 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.379 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.379 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.379 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.379 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.379 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.379 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.381 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.381 INFO  ProgressMeter - Starting traversal
19:01:57.381 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.382 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.382 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.382 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.382 INFO  ProgressMeter -             unmapped              0.0                    16         960000.0
19:01:57.382 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
19:01:57.382 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.398 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.398 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.398 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.398 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.398 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.398 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.398 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.398 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.398 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.398 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.398 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.398 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.398 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.398 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.398 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.398 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.398 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.400 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.400 INFO  ProgressMeter - Starting traversal
19:01:57.400 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.402 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.403 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.403 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.403 INFO  ProgressMeter -             unmapped              0.0                    16         320000.0
19:01:57.403 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
19:01:57.403 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864
19:01:57.418 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.419 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:01:57.419 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:57.419 INFO  dummyMultiplePassReadWalker - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:57.419 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:57.419 INFO  dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 7:01:57 PM GMT
19:01:57.419 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.419 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
19:01:57.419 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:57.419 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:57.419 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:57.419 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:57.419 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
19:01:57.419 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
19:01:57.419 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
19:01:57.419 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
19:01:57.419 INFO  dummyMultiplePassReadWalker - Initializing engine
19:01:57.420 INFO  dummyMultiplePassReadWalker - Done initializing engine
19:01:57.420 INFO  ProgressMeter - Starting traversal
19:01:57.420 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:01:57.424 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.424 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
19:01:57.426 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

19:01:57.426 INFO  ProgressMeter -             unmapped              0.0                    16         160000.0
19:01:57.426 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
19:01:57.427 INFO  dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 7:01:57 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1115684864