Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.874s |
passed |
| testBasicBQ |
0.665s |
passed |
Standard error
14:27:43.545 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:27:43.545 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
14:27:43.545 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
14:27:43.545 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:27:43.545 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:27:43.545 INFO AddFlowSNVQuality - Start Date/Time: June 2, 2025 at 2:27:43 PM UTC
14:27:43.545 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:27:43.545 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:27:43.546 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:27:43.546 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:27:43.546 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:27:43.546 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:27:43.546 INFO AddFlowSNVQuality - Deflater: IntelDeflater
14:27:43.546 INFO AddFlowSNVQuality - Inflater: IntelInflater
14:27:43.546 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
14:27:43.546 INFO AddFlowSNVQuality - Requester pays: disabled
14:27:43.546 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:27:43.546 INFO AddFlowSNVQuality - Initializing engine
14:27:43.607 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
14:27:43.608 INFO AddFlowSNVQuality - Done initializing engine
14:27:43.618 INFO ProgressMeter - Starting traversal
14:27:43.618 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:27:44.273 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
14:27:44.273 INFO ProgressMeter - chr1:14608 0.0 4278 391877.9
14:27:44.273 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
14:27:44.323 INFO AddFlowSNVQuality - Shutting down engine
[June 2, 2025 at 2:27:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
14:27:44.422 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:27:44.422 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
14:27:44.422 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
14:27:44.422 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:27:44.422 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:27:44.422 INFO AddFlowSNVQuality - Start Date/Time: June 2, 2025 at 2:27:44 PM UTC
14:27:44.422 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:27:44.422 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:27:44.422 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:27:44.422 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:27:44.422 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:27:44.422 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:27:44.422 INFO AddFlowSNVQuality - Deflater: IntelDeflater
14:27:44.422 INFO AddFlowSNVQuality - Inflater: IntelInflater
14:27:44.422 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
14:27:44.422 INFO AddFlowSNVQuality - Requester pays: disabled
14:27:44.422 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:27:44.422 INFO AddFlowSNVQuality - Initializing engine
14:27:44.482 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
14:27:44.483 INFO AddFlowSNVQuality - Done initializing engine
14:27:44.492 INFO ProgressMeter - Starting traversal
14:27:44.492 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:27:44.932 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
14:27:44.932 INFO ProgressMeter - chr1:14608 0.0 4278 583363.6
14:27:44.932 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
14:27:44.986 INFO AddFlowSNVQuality - Shutting down engine
[June 2, 2025 at 2:27:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536