Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
1.029s |
passed |
| testBasicBQ |
0.542s |
passed |
Standard error
16:41:08.538 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:41:08.538 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
16:41:08.538 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
16:41:08.538 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
16:41:08.538 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
16:41:08.538 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 4:41:08 PM UTC
16:41:08.538 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:41:08.538 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:41:08.539 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:41:08.539 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:41:08.539 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:41:08.539 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:41:08.539 INFO AddFlowSNVQuality - Deflater: IntelDeflater
16:41:08.539 INFO AddFlowSNVQuality - Inflater: IntelInflater
16:41:08.539 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
16:41:08.539 INFO AddFlowSNVQuality - Requester pays: disabled
16:41:08.539 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:41:08.539 INFO AddFlowSNVQuality - Initializing engine
16:41:08.599 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
16:41:08.600 INFO AddFlowSNVQuality - Done initializing engine
16:41:08.610 INFO ProgressMeter - Starting traversal
16:41:08.610 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:41:09.432 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
16:41:09.432 INFO ProgressMeter - chr1:14608 0.0 4278 312262.8
16:41:09.432 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
16:41:09.482 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 4:41:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1954545664
16:41:09.574 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:41:09.574 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
16:41:09.574 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
16:41:09.574 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
16:41:09.574 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
16:41:09.574 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 4:41:09 PM UTC
16:41:09.574 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:41:09.574 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:41:09.574 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:41:09.574 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:41:09.574 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:41:09.574 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:41:09.574 INFO AddFlowSNVQuality - Deflater: IntelDeflater
16:41:09.574 INFO AddFlowSNVQuality - Inflater: IntelInflater
16:41:09.574 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
16:41:09.574 INFO AddFlowSNVQuality - Requester pays: disabled
16:41:09.574 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:41:09.574 INFO AddFlowSNVQuality - Initializing engine
16:41:09.634 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
16:41:09.635 INFO AddFlowSNVQuality - Done initializing engine
16:41:09.644 INFO ProgressMeter - Starting traversal
16:41:09.644 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:41:09.971 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
16:41:09.971 INFO ProgressMeter - chr1:14608 0.0 4278 784954.1
16:41:09.971 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
16:41:10.022 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 4:41:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1954545664