Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0.001s |
passed |
| testBasic |
0.786s |
passed |
| testBasicBQ |
0.532s |
passed |
Standard error
13:55:35.633 INFO AddFlowSNVQuality - ------------------------------------------------------------
13:55:35.633 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
13:55:35.633 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
13:55:35.633 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:55:35.633 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:55:35.633 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 1:55:35 PM UTC
13:55:35.633 INFO AddFlowSNVQuality - ------------------------------------------------------------
13:55:35.633 INFO AddFlowSNVQuality - ------------------------------------------------------------
13:55:35.633 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:55:35.633 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:55:35.633 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:55:35.633 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:55:35.633 INFO AddFlowSNVQuality - Deflater: IntelDeflater
13:55:35.633 INFO AddFlowSNVQuality - Inflater: IntelInflater
13:55:35.633 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
13:55:35.633 INFO AddFlowSNVQuality - Requester pays: disabled
13:55:35.633 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
13:55:35.633 INFO AddFlowSNVQuality - Initializing engine
13:55:35.692 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
13:55:35.693 INFO AddFlowSNVQuality - Done initializing engine
13:55:35.702 INFO ProgressMeter - Starting traversal
13:55:35.702 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
13:55:36.285 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
13:55:36.285 INFO ProgressMeter - chr1:14608 0.0 4278 440274.4
13:55:36.285 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
13:55:36.335 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 1:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
13:55:36.422 INFO AddFlowSNVQuality - ------------------------------------------------------------
13:55:36.422 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
13:55:36.422 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
13:55:36.422 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:55:36.422 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:55:36.422 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 1:55:36 PM UTC
13:55:36.422 INFO AddFlowSNVQuality - ------------------------------------------------------------
13:55:36.422 INFO AddFlowSNVQuality - ------------------------------------------------------------
13:55:36.422 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:55:36.422 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:55:36.422 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:55:36.422 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:55:36.422 INFO AddFlowSNVQuality - Deflater: IntelDeflater
13:55:36.422 INFO AddFlowSNVQuality - Inflater: IntelInflater
13:55:36.422 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
13:55:36.422 INFO AddFlowSNVQuality - Requester pays: disabled
13:55:36.422 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
13:55:36.422 INFO AddFlowSNVQuality - Initializing engine
13:55:36.479 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
13:55:36.480 INFO AddFlowSNVQuality - Done initializing engine
13:55:36.489 INFO ProgressMeter - Starting traversal
13:55:36.489 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
13:55:36.814 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
13:55:36.815 INFO ProgressMeter - chr1:14608 0.0 4278 787362.0
13:55:36.815 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
13:55:36.865 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 1:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288