Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.897s |
passed |
| testBasicBQ |
0.513s |
passed |
Standard error
18:21:03.504 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:21:03.504 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
18:21:03.504 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
18:21:03.504 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:21:03.504 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:21:03.504 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 6:21:03 PM UTC
18:21:03.504 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:21:03.504 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:21:03.504 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:21:03.504 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:21:03.504 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:21:03.504 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:21:03.504 INFO AddFlowSNVQuality - Deflater: IntelDeflater
18:21:03.504 INFO AddFlowSNVQuality - Inflater: IntelInflater
18:21:03.504 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
18:21:03.504 INFO AddFlowSNVQuality - Requester pays: disabled
18:21:03.504 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:21:03.504 INFO AddFlowSNVQuality - Initializing engine
18:21:03.566 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
18:21:03.567 INFO AddFlowSNVQuality - Done initializing engine
18:21:03.583 INFO ProgressMeter - Starting traversal
18:21:03.584 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:21:04.268 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
18:21:04.268 INFO ProgressMeter - chr1:14608 0.0 4278 375263.2
18:21:04.268 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
18:21:04.318 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 6:21:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1956642816
18:21:04.403 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:21:04.403 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
18:21:04.403 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
18:21:04.403 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:21:04.403 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:21:04.403 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 6:21:04 PM UTC
18:21:04.403 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:21:04.403 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:21:04.403 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:21:04.403 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:21:04.403 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:21:04.403 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:21:04.403 INFO AddFlowSNVQuality - Deflater: IntelDeflater
18:21:04.403 INFO AddFlowSNVQuality - Inflater: IntelInflater
18:21:04.403 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
18:21:04.403 INFO AddFlowSNVQuality - Requester pays: disabled
18:21:04.403 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:21:04.403 INFO AddFlowSNVQuality - Initializing engine
18:21:04.461 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
18:21:04.462 INFO AddFlowSNVQuality - Done initializing engine
18:21:04.470 INFO ProgressMeter - Starting traversal
18:21:04.470 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:21:04.779 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
18:21:04.779 INFO ProgressMeter - chr1:14608 0.0 4278 830679.6
18:21:04.779 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
18:21:04.829 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 6:21:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1956642816