Class org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest

all > org.broadinstitute.hellbender.engine > MultiplePassReadWalkerUnitTest
tests
failures
ignored
0.288s
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)	0.029s	passed
testPassCounts[0](0)	0.018s	passed
testPassCounts[1](1)	0.016s	passed
testPassCounts[2](2)	0.017s	passed
testPassCounts[3](5)	0.019s	passed
testPassCounts[4](25)	0.024s	passed
testRejectAttemptToIndexNonIndexableInput[0](/count_reads.bam)	0.028s	passed
testRejectAttemptToIndexNonIndexableInput[1](/count_reads.sam)	0.026s	passed
testRejectAttemptToIndexNonIndexableInput[2](/count_reads.cram)	0.018s	passed
testTwoPass[0](/count_reads.bam)	0.024s	passed
testTwoPass[1](/count_reads.sam)	0.018s	passed
testTwoPass[2](/count_reads.cram)	0.021s	passed
Standard error

20:25:22.125 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.125 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.125 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.126 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.126 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.126 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.126 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.126 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.126 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.126 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.126 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.126 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.126 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.126 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.126 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.126 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.126 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.132 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:25:22.132 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.132 INFO  ProgressMeter - Starting traversal
20:25:22.132 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.134 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.134 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.134 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.134 INFO  ProgressMeter -             unmapped              0.0                    10         300000.0
20:25:22.135 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
20:25:22.135 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.150 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.150 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.150 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.150 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.150 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.150 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.150 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.150 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.150 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.150 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.150 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.150 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.150 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.150 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.150 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.150 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.150 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.156 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:25:22.156 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.156 INFO  ProgressMeter - Starting traversal
20:25:22.156 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.161 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.162 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.163 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.163 INFO  ProgressMeter -             unmapped              0.0                    10          85714.3
20:25:22.163 INFO  ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
20:25:22.163 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.180 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.180 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.180 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.180 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.180 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.180 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.180 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.180 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.180 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.180 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.180 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.180 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.180 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.180 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.180 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.180 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.180 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.181 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.181 INFO  ProgressMeter - Starting traversal
20:25:22.181 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.181 INFO  ProgressMeter -             unmapped              0.0                     0              NaN
20:25:22.181 INFO  ProgressMeter - Traversal complete. Processed 0 total reads in 0.0 minutes.
20:25:22.181 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.196 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.196 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.196 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.196 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.196 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.196 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.196 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.196 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.196 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.196 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.196 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.196 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.196 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.196 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.196 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.196 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.196 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.197 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.197 INFO  ProgressMeter - Starting traversal
20:25:22.197 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.198 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.198 INFO  ProgressMeter -             unmapped              0.0                     8         480000.0
20:25:22.198 INFO  ProgressMeter - Traversal complete. Processed 8 total reads in 0.0 minutes.
20:25:22.198 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.213 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.213 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.213 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.213 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.213 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.213 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.213 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.213 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.213 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.213 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.213 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.213 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.213 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.213 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.213 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.213 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.213 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.214 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.214 INFO  ProgressMeter - Starting traversal
20:25:22.214 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.214 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.215 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.215 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.215 INFO  ProgressMeter -             unmapped              0.0                    16         960000.0
20:25:22.215 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:25:22.215 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.230 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.230 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.230 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.230 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.230 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.230 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.230 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.230 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.230 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.230 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.230 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.230 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.230 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.230 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.230 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.230 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.230 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.231 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.231 INFO  ProgressMeter - Starting traversal
20:25:22.231 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.231 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.232 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.232 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.232 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
20:25:22.232 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.232 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
20:25:22.233 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.233 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
20:25:22.233 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.233 INFO  ProgressMeter -             unmapped              0.0                    40        1200000.0
20:25:22.233 INFO  ProgressMeter - Traversal complete. Processed 40 total reads in 0.0 minutes.
20:25:22.233 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.250 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.250 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.250 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.250 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.250 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.250 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.250 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.250 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.250 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.250 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.250 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.250 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.250 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.250 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.250 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.250 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.250 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.251 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.251 INFO  ProgressMeter - Starting traversal
20:25:22.251 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.252 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.252 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.252 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.252 INFO  dummyMultiplePassReadWalker - Starting traversal pass 3
20:25:22.252 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.252 INFO  dummyMultiplePassReadWalker - Starting traversal pass 4
20:25:22.252 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.252 INFO  dummyMultiplePassReadWalker - Starting traversal pass 5
20:25:22.253 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.253 INFO  dummyMultiplePassReadWalker - Starting traversal pass 6
20:25:22.253 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.253 INFO  dummyMultiplePassReadWalker - Starting traversal pass 7
20:25:22.253 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.253 INFO  dummyMultiplePassReadWalker - Starting traversal pass 8
20:25:22.253 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.253 INFO  dummyMultiplePassReadWalker - Starting traversal pass 9
20:25:22.253 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.254 INFO  dummyMultiplePassReadWalker - Starting traversal pass 10
20:25:22.254 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.254 INFO  dummyMultiplePassReadWalker - Starting traversal pass 11
20:25:22.254 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.254 INFO  dummyMultiplePassReadWalker - Starting traversal pass 12
20:25:22.254 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.254 INFO  dummyMultiplePassReadWalker - Starting traversal pass 13
20:25:22.254 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.254 INFO  dummyMultiplePassReadWalker - Starting traversal pass 14
20:25:22.255 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.255 INFO  dummyMultiplePassReadWalker - Starting traversal pass 15
20:25:22.255 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.255 INFO  dummyMultiplePassReadWalker - Starting traversal pass 16
20:25:22.255 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.255 INFO  dummyMultiplePassReadWalker - Starting traversal pass 17
20:25:22.255 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.255 INFO  dummyMultiplePassReadWalker - Starting traversal pass 18
20:25:22.256 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.256 INFO  dummyMultiplePassReadWalker - Starting traversal pass 19
20:25:22.256 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.256 INFO  dummyMultiplePassReadWalker - Starting traversal pass 20
20:25:22.256 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.256 INFO  dummyMultiplePassReadWalker - Starting traversal pass 21
20:25:22.256 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.256 INFO  dummyMultiplePassReadWalker - Starting traversal pass 22
20:25:22.256 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.256 INFO  dummyMultiplePassReadWalker - Starting traversal pass 23
20:25:22.257 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.257 INFO  dummyMultiplePassReadWalker - Starting traversal pass 24
20:25:22.257 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.257 INFO  dummyMultiplePassReadWalker - Starting traversal pass 25
20:25:22.257 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.257 INFO  ProgressMeter -             unmapped              0.0                   200        2000000.0
20:25:22.257 INFO  ProgressMeter - Traversal complete. Processed 200 total reads in 0.0 minutes.
20:25:22.257 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.280 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.280 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.280 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.280 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.280 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.280 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.280 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.280 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.280 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.280 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.280 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.280 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.280 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.280 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.280 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.280 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.280 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.285 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:25:22.286 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.306 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.306 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.306 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.306 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.306 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.306 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.306 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.306 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.306 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.306 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.306 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.306 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.306 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.306 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.306 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.306 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.306 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.311 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:25:22.311 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.326 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.326 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.326 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.326 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.326 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.326 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.326 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.326 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.326 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.326 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.326 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.326 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.326 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.326 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.326 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.326 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.326 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.329 INFO  IntervalArgumentCollection - Processing 31 bp from intervals
20:25:22.330 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.351 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.351 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.351 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.351 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.351 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.351 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.352 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.352 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.352 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.352 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.352 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.352 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.352 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.352 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.352 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.352 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.352 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.353 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.353 INFO  ProgressMeter - Starting traversal
20:25:22.353 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.353 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.353 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.353 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.353 INFO  ProgressMeter -             unmapped              0.0                    16         Infinity
20:25:22.353 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:25:22.353 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.368 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.368 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.368 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.368 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.368 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.368 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.368 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.368 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.368 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.368 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.368 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.368 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.368 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.368 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.368 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.368 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.368 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.369 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.369 INFO  ProgressMeter - Starting traversal
20:25:22.369 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.371 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.372 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.372 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.372 INFO  ProgressMeter -             unmapped              0.0                    16         320000.0
20:25:22.372 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:25:22.372 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408
20:25:22.387 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.387 INFO  dummyMultiplePassReadWalker - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-gb2a05c7-SNAPSHOT
20:25:22.387 INFO  dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:22.387 INFO  dummyMultiplePassReadWalker - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:22.387 INFO  dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:22.387 INFO  dummyMultiplePassReadWalker - Start Date/Time: February 10, 2025 at 8:25:22 PM GMT
20:25:22.387 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.387 INFO  dummyMultiplePassReadWalker - ------------------------------------------------------------
20:25:22.387 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:22.387 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:22.387 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:22.387 INFO  dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:22.387 INFO  dummyMultiplePassReadWalker - Deflater: IntelDeflater
20:25:22.387 INFO  dummyMultiplePassReadWalker - Inflater: IntelInflater
20:25:22.387 INFO  dummyMultiplePassReadWalker - GCS max retries/reopens: 20
20:25:22.387 INFO  dummyMultiplePassReadWalker - Requester pays: disabled
20:25:22.387 INFO  dummyMultiplePassReadWalker - Initializing engine
20:25:22.388 INFO  dummyMultiplePassReadWalker - Done initializing engine
20:25:22.388 INFO  ProgressMeter - Starting traversal
20:25:22.388 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:25:22.391 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.391 INFO  dummyMultiplePassReadWalker - Starting traversal pass 2
20:25:22.393 INFO  dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter 

20:25:22.393 INFO  ProgressMeter -             unmapped              0.0                    16         192000.0
20:25:22.393 INFO  ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
20:25:22.393 INFO  dummyMultiplePassReadWalker - Shutting down engine
[February 10, 2025 at 8:25:22 PM GMT] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1109393408