Class org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest
Tests
| Test |
Duration |
Result |
| testIntervalFiltering[0](/count_reads_sorted.bam) |
0.013s |
passed |
| testIntervalFiltering[1](/count_reads_sorted.cram) |
0.016s |
passed |
| testPassCounts[0](0) |
0.008s |
passed |
| testPassCounts[1](1) |
0.006s |
passed |
| testPassCounts[2](2) |
0.006s |
passed |
| testPassCounts[3](5) |
0.007s |
passed |
| testPassCounts[4](25) |
0.011s |
passed |
| testRejectAttemptToIndexNonIndexableInput[0](/count_reads.bam) |
0.012s |
passed |
| testRejectAttemptToIndexNonIndexableInput[1](/count_reads.sam) |
0.009s |
passed |
| testRejectAttemptToIndexNonIndexableInput[2](/count_reads.cram) |
0.007s |
passed |
| testTwoPass[0](/count_reads.bam) |
0.007s |
passed |
| testTwoPass[1](/count_reads.sam) |
0.012s |
passed |
| testTwoPass[2](/count_reads.cram) |
0.013s |
passed |
Standard error
18:46:04.636 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.636 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.636 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.636 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.636 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.636 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.636 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.636 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.637 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.637 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.637 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.637 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.637 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.637 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.637 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.637 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.637 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.642 INFO IntervalArgumentCollection - Processing 31 bp from intervals
18:46:04.642 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.642 INFO ProgressMeter - Starting traversal
18:46:04.642 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.643 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.644 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.644 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.644 INFO ProgressMeter - unmapped 0.0 10 300000.0
18:46:04.644 INFO ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
18:46:04.644 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.649 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.649 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.649 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.649 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.649 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.649 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.649 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.649 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.649 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.649 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.649 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.649 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.649 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.649 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.649 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.650 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.650 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.654 INFO IntervalArgumentCollection - Processing 31 bp from intervals
18:46:04.654 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.654 INFO ProgressMeter - Starting traversal
18:46:04.654 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.659 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.659 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.660 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.660 INFO ProgressMeter - unmapped 0.0 10 100000.0
18:46:04.660 INFO ProgressMeter - Traversal complete. Processed 10 total reads in 0.0 minutes.
18:46:04.660 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.668 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.668 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.668 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.668 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.668 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.668 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.668 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.668 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.668 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.668 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.668 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.668 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.668 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.668 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.668 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.668 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.668 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.669 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.669 INFO ProgressMeter - Starting traversal
18:46:04.669 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.669 INFO ProgressMeter - unmapped 0.0 0 NaN
18:46:04.669 INFO ProgressMeter - Traversal complete. Processed 0 total reads in 0.0 minutes.
18:46:04.669 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.675 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.675 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.675 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.675 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.675 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.675 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.675 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.675 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.675 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.675 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.675 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.675 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.675 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.675 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.675 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.675 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.675 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.675 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.676 INFO ProgressMeter - Starting traversal
18:46:04.676 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.676 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.676 INFO ProgressMeter - unmapped 0.0 8 Infinity
18:46:04.676 INFO ProgressMeter - Traversal complete. Processed 8 total reads in 0.0 minutes.
18:46:04.676 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.681 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.681 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.681 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.681 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.681 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.681 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.681 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.681 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.681 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.681 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.681 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.681 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.681 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.681 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.681 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.681 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.681 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.682 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.682 INFO ProgressMeter - Starting traversal
18:46:04.682 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.682 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.682 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.682 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.682 INFO ProgressMeter - unmapped 0.0 16 Infinity
18:46:04.683 INFO ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
18:46:04.683 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.687 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.687 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.687 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.687 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.687 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.687 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.687 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.687 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.687 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.687 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.687 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.687 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.687 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.687 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.687 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.687 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.687 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.688 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.688 INFO ProgressMeter - Starting traversal
18:46:04.688 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.688 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.688 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.689 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.689 INFO dummyMultiplePassReadWalker - Starting traversal pass 3
18:46:04.689 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.689 INFO dummyMultiplePassReadWalker - Starting traversal pass 4
18:46:04.689 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.689 INFO dummyMultiplePassReadWalker - Starting traversal pass 5
18:46:04.689 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.690 INFO ProgressMeter - unmapped 0.0 40 1200000.0
18:46:04.690 INFO ProgressMeter - Traversal complete. Processed 40 total reads in 0.0 minutes.
18:46:04.690 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.694 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.694 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.694 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.694 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.694 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.694 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.694 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.694 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.694 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.694 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.694 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.694 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.694 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.694 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.694 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.694 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.694 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.695 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.695 INFO ProgressMeter - Starting traversal
18:46:04.695 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.695 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.695 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.695 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.695 INFO dummyMultiplePassReadWalker - Starting traversal pass 3
18:46:04.696 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.696 INFO dummyMultiplePassReadWalker - Starting traversal pass 4
18:46:04.696 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.696 INFO dummyMultiplePassReadWalker - Starting traversal pass 5
18:46:04.696 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.696 INFO dummyMultiplePassReadWalker - Starting traversal pass 6
18:46:04.696 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.696 INFO dummyMultiplePassReadWalker - Starting traversal pass 7
18:46:04.696 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.696 INFO dummyMultiplePassReadWalker - Starting traversal pass 8
18:46:04.697 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.697 INFO dummyMultiplePassReadWalker - Starting traversal pass 9
18:46:04.697 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.697 INFO dummyMultiplePassReadWalker - Starting traversal pass 10
18:46:04.697 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.697 INFO dummyMultiplePassReadWalker - Starting traversal pass 11
18:46:04.697 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.697 INFO dummyMultiplePassReadWalker - Starting traversal pass 12
18:46:04.698 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.698 INFO dummyMultiplePassReadWalker - Starting traversal pass 13
18:46:04.698 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.698 INFO dummyMultiplePassReadWalker - Starting traversal pass 14
18:46:04.698 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.698 INFO dummyMultiplePassReadWalker - Starting traversal pass 15
18:46:04.698 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.698 INFO dummyMultiplePassReadWalker - Starting traversal pass 16
18:46:04.699 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.699 INFO dummyMultiplePassReadWalker - Starting traversal pass 17
18:46:04.699 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.699 INFO dummyMultiplePassReadWalker - Starting traversal pass 18
18:46:04.699 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.699 INFO dummyMultiplePassReadWalker - Starting traversal pass 19
18:46:04.699 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.699 INFO dummyMultiplePassReadWalker - Starting traversal pass 20
18:46:04.699 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.699 INFO dummyMultiplePassReadWalker - Starting traversal pass 21
18:46:04.700 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.700 INFO dummyMultiplePassReadWalker - Starting traversal pass 22
18:46:04.700 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.700 INFO dummyMultiplePassReadWalker - Starting traversal pass 23
18:46:04.700 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.700 INFO dummyMultiplePassReadWalker - Starting traversal pass 24
18:46:04.700 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.700 INFO dummyMultiplePassReadWalker - Starting traversal pass 25
18:46:04.700 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.700 INFO ProgressMeter - unmapped 0.0 200 2400000.0
18:46:04.700 INFO ProgressMeter - Traversal complete. Processed 200 total reads in 0.0 minutes.
18:46:04.700 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.708 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.708 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.708 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.708 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.708 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.708 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.708 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.708 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.708 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.708 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.708 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.708 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.708 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.708 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.708 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.708 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.708 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.711 INFO IntervalArgumentCollection - Processing 31 bp from intervals
18:46:04.712 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.718 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.718 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.718 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.718 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.718 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.718 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.718 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.718 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.718 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.718 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.718 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.718 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.718 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.718 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.718 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.718 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.718 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.722 INFO IntervalArgumentCollection - Processing 31 bp from intervals
18:46:04.722 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.726 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.726 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.726 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.726 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.726 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.726 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.726 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.726 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.726 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.726 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.726 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.726 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.726 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.726 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.726 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.726 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.726 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.729 INFO IntervalArgumentCollection - Processing 31 bp from intervals
18:46:04.729 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.734 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.734 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.734 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.734 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.734 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.734 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.734 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.734 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.734 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.734 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.734 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.734 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.734 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.734 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.734 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.734 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.735 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.736 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.736 INFO ProgressMeter - Starting traversal
18:46:04.736 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.736 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.736 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.737 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.737 INFO ProgressMeter - unmapped 0.0 16 960000.0
18:46:04.737 INFO ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
18:46:04.737 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.743 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.743 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.743 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.743 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.743 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.743 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.743 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.743 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.743 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.743 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.743 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.743 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.743 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.743 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.743 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.743 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.743 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.744 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.744 INFO ProgressMeter - Starting traversal
18:46:04.744 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.747 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.748 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.748 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.748 INFO ProgressMeter - unmapped 0.0 16 240000.0
18:46:04.748 INFO ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
18:46:04.748 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
18:46:04.754 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.754 INFO dummyMultiplePassReadWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.754 INFO dummyMultiplePassReadWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.754 INFO dummyMultiplePassReadWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.754 INFO dummyMultiplePassReadWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.754 INFO dummyMultiplePassReadWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.754 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.754 INFO dummyMultiplePassReadWalker - ------------------------------------------------------------
18:46:04.755 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.755 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.755 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.755 INFO dummyMultiplePassReadWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.755 INFO dummyMultiplePassReadWalker - Deflater: IntelDeflater
18:46:04.755 INFO dummyMultiplePassReadWalker - Inflater: IntelInflater
18:46:04.755 INFO dummyMultiplePassReadWalker - GCS max retries/reopens: 20
18:46:04.755 INFO dummyMultiplePassReadWalker - Requester pays: disabled
18:46:04.755 INFO dummyMultiplePassReadWalker - Initializing engine
18:46:04.756 INFO dummyMultiplePassReadWalker - Done initializing engine
18:46:04.756 INFO ProgressMeter - Starting traversal
18:46:04.756 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:46:04.760 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.760 INFO dummyMultiplePassReadWalker - Starting traversal pass 2
18:46:04.761 INFO dummyMultiplePassReadWalker - 0 read(s) filtered by: WellformedReadFilter
18:46:04.762 INFO ProgressMeter - unmapped 0.0 16 160000.0
18:46:04.762 INFO ProgressMeter - Traversal complete. Processed 16 total reads in 0.0 minutes.
18:46:04.762 INFO dummyMultiplePassReadWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassReadWalkerUnitTest$dummyMultiplePassReadWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600