Class org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest

all > org.broadinstitute.hellbender.engine > MultiplePassReadWalkerUnitTest
tests
failures
ignored
0.349s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testIntervalFiltering[0](/count_reads_sorted.bam)	0.030s	passed
testIntervalFiltering[1](/count_reads_sorted.cram)	0.035s	passed
testPassCounts[0](0)	0.023s	passed
testPassCounts[1](1)	0.025s	passed
testPassCounts[2](2)	0.023s	passed
testPassCounts[3](5)	0.030s	passed
testPassCounts[4](25)	0.030s	passed
testRejectAttemptToIndexNonIndexableInput[0](/count_reads.bam)	0.026s	passed
testRejectAttemptToIndexNonIndexableInput[1](/count_reads.sam)	0.026s	passed
testRejectAttemptToIndexNonIndexableInput[2](/count_reads.cram)	0.024s	passed
testTwoPass[0](/count_reads.bam)	0.023s	passed
testTwoPass[1](/count_reads.sam)	0.026s	passed
testTwoPass[2](/count_reads.cram)	0.028s	passed
Standard error

22:03:39.170 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.170 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.170 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.171 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.171 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.171 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.171 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.171 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.171 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.171 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.171 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.171 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.171 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.171 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.177 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
22:03:39.177 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.177 INFO  ProgressMeter - Starting traversal
22:03:39.177 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.179 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.179 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.180 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.180 INFO  ProgressMeter -             unmapped              0.0                    10         200000.0
22:03:39.180 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
22:03:39.180 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.201 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.201 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.201 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.201 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.201 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.201 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.201 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.201 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.201 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.201 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.201 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.201 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.201 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.201 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.201 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.201 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.201 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.207 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
22:03:39.207 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.207 INFO  ProgressMeter - Starting traversal
22:03:39.207 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.213 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.213 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.214 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.215 INFO  ProgressMeter -             unmapped              0.0                    10          85714.3
22:03:39.215 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
22:03:39.215 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.237 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.237 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.237 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.237 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.237 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.237 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.237 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.237 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.237 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.237 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.237 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.237 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.238 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.238 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.238 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.238 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.238 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.239 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.239 INFO  ProgressMeter - Starting traversal
22:03:39.239 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.239 INFO  ProgressMeter -             unmapped              0.0                     0              NaN
22:03:39.239 INFO  ProgressMeter - Traversal complete. Processed 0 total reads in 0.0 minutes.
22:03:39.239 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.261 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.261 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.261 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.261 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.261 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.261 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.262 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.262 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.262 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.262 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.262 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.262 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.262 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.262 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.262 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.262 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.262 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.263 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.263 INFO  ProgressMeter - Starting traversal
22:03:39.263 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.263 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.263 INFO  ProgressMeter -             unmapped              0.0                     8         Infinity
22:03:39.264 INFO  ProgressMeter - Traversal complete. Processed 8 total reads in 0.0 minutes.
22:03:39.264 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.284 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.284 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.284 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.284 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.284 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.284 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.284 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.284 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.284 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.284 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.284 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.284 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.284 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.285 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.285 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.285 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.285 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.285 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.285 INFO  ProgressMeter - Starting traversal
22:03:39.285 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.286 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.286 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.286 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.287 INFO  ProgressMeter -             unmapped              0.0                    16         960000.0
22:03:39.287 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
22:03:39.287 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.313 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.314 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.314 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.314 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.314 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.314 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.314 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.314 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.314 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.314 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.314 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.314 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.314 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.314 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.315 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.315 INFO  ProgressMeter - Starting traversal
22:03:39.315 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.315 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.315 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.316 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.316 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
22:03:39.316 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.316 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
22:03:39.317 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.317 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
22:03:39.317 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.317 INFO  ProgressMeter -             unmapped              0.0                    40        1200000.0
22:03:39.317 INFO  ProgressMeter - Traversal complete. Processed 40 total reads in 0.0 minutes.
22:03:39.317 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.338 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.338 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.338 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.338 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.338 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.338 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.338 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.339 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.339 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.339 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.339 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.339 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.339 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.339 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.339 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.339 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.339 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.339 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.340 INFO  ProgressMeter - Starting traversal
22:03:39.340 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.340 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.340 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.340 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.340 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
22:03:39.341 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.341 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
22:03:39.341 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.341 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
22:03:39.342 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.342 INFO  dummyMultiplePassReadWalker - Starting traversal pass 6
22:03:39.342 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.342 INFO  dummyMultiplePassReadWalker - Starting traversal pass 7
22:03:39.343 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.343 INFO  dummyMultiplePassReadWalker - Starting traversal pass 8
22:03:39.343 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.343 INFO  dummyMultiplePassReadWalker - Starting traversal pass 9
22:03:39.343 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.344 INFO  dummyMultiplePassReadWalker - Starting traversal pass 10
22:03:39.344 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.344 INFO  dummyMultiplePassReadWalker - Starting traversal pass 11
22:03:39.344 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.344 INFO  dummyMultiplePassReadWalker - Starting traversal pass 12
22:03:39.344 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.344 INFO  dummyMultiplePassReadWalker - Starting traversal pass 13
22:03:39.344 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.344 INFO  dummyMultiplePassReadWalker - Starting traversal pass 14
22:03:39.344 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.344 INFO  dummyMultiplePassReadWalker - Starting traversal pass 15
22:03:39.344 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.344 INFO  dummyMultiplePassReadWalker - Starting traversal pass 16
22:03:39.345 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.345 INFO  dummyMultiplePassReadWalker - Starting traversal pass 17
22:03:39.345 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.345 INFO  dummyMultiplePassReadWalker - Starting traversal pass 18
22:03:39.345 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.345 INFO  dummyMultiplePassReadWalker - Starting traversal pass 19
22:03:39.345 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.345 INFO  dummyMultiplePassReadWalker - Starting traversal pass 20
22:03:39.345 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.345 INFO  dummyMultiplePassReadWalker - Starting traversal pass 21
22:03:39.345 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.345 INFO  dummyMultiplePassReadWalker - Starting traversal pass 22
22:03:39.346 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.346 INFO  dummyMultiplePassReadWalker - Starting traversal pass 23
22:03:39.346 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.347 INFO  dummyMultiplePassReadWalker - Starting traversal pass 24
22:03:39.347 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.347 INFO  dummyMultiplePassReadWalker - Starting traversal pass 25
22:03:39.347 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.347 INFO  ProgressMeter -             unmapped              0.0                   200        1714285.7
22:03:39.347 INFO  ProgressMeter - Traversal complete. Processed 200 total reads in 0.0 minutes.
22:03:39.347 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.369 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.369 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.369 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.369 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.369 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.369 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.369 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.369 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.369 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.369 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.369 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.369 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.369 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.369 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.369 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.369 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.369 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.373 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
22:03:39.374 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.394 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.394 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.394 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.394 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.394 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.394 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.394 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.394 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.394 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.394 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.394 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.394 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.394 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.394 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.394 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.394 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.394 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.399 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
22:03:39.399 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.420 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.420 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.420 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.420 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.420 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.420 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.420 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.420 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.420 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.420 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.420 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.420 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.420 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.420 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.420 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.420 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.420 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.424 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
22:03:39.424 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.445 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.445 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.445 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.445 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.445 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.445 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.445 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.445 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.445 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.445 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.445 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.445 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.446 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.446 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.446 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.446 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.446 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.447 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.447 INFO  ProgressMeter - Starting traversal
22:03:39.447 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.447 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.447 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.448 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.448 INFO  ProgressMeter -             unmapped              0.0                    16         960000.0
22:03:39.448 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
22:03:39.448 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.468 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.468 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.468 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.468 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.468 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.468 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.468 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.468 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.468 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.468 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.468 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.468 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.468 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.468 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.468 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.468 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.468 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.470 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.470 INFO  ProgressMeter - Starting traversal
22:03:39.470 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.472 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.473 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.474 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.474 INFO  ProgressMeter -             unmapped              0.0                    16         240000.0
22:03:39.474 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
22:03:39.474 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968
22:03:39.495 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.495 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-2-gfa08e16-SNAPSHOT
22:03:39.495 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:39.495 INFO  dummyMultiplePassReadWalker - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:39.495 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:39.495 INFO  dummyMultiplePassReadWalker - Start Date/Time: April 22, 2025 at 10:03:39 PM GMT
22:03:39.495 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.495 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
22:03:39.495 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:39.495 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:39.495 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:39.495 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:39.495 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
22:03:39.495 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
22:03:39.495 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
22:03:39.495 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
22:03:39.495 INFO  dummyMultiplePassReadWalker - Initializing engine
22:03:39.497 INFO  dummyMultiplePassReadWalker - Done initializing engine
22:03:39.497 INFO  ProgressMeter - Starting traversal
22:03:39.497 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:03:39.500 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.501 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
22:03:39.503 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

22:03:39.503 INFO  ProgressMeter -             unmapped              0.0                    16         160000.0
22:03:39.503 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
22:03:39.503 INFO  dummyMultiplePassReadWalker - Shutting down engine
[April 22, 2025 at 10:03:39 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=910163968