Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.967s |
passed |
| testBasicBQ |
0.711s |
passed |
Standard error
21:06:47.576 INFO AddFlowSNVQuality - ------------------------------------------------------------
21:06:47.576 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:06:47.576 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
21:06:47.576 INFO AddFlowSNVQuality - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:06:47.576 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:06:47.576 INFO AddFlowSNVQuality - Start Date/Time: June 12, 2025 at 9:06:47 PM GMT
21:06:47.576 INFO AddFlowSNVQuality - ------------------------------------------------------------
21:06:47.576 INFO AddFlowSNVQuality - ------------------------------------------------------------
21:06:47.576 INFO AddFlowSNVQuality - HTSJDK Version: 4.2.0
21:06:47.576 INFO AddFlowSNVQuality - Picard Version: 3.4.0
21:06:47.576 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
21:06:47.576 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:06:47.576 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:06:47.576 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:06:47.576 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:06:47.576 INFO AddFlowSNVQuality - Deflater: IntelDeflater
21:06:47.576 INFO AddFlowSNVQuality - Inflater: IntelInflater
21:06:47.576 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
21:06:47.576 INFO AddFlowSNVQuality - Requester pays: disabled
21:06:47.576 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
21:06:47.576 INFO AddFlowSNVQuality - Initializing engine
21:06:47.635 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
21:06:47.636 INFO AddFlowSNVQuality - Done initializing engine
21:06:47.644 INFO ProgressMeter - Starting traversal
21:06:47.644 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
21:06:48.373 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
21:06:48.373 INFO ProgressMeter - chr1:14608 0.0 4278 352098.8
21:06:48.374 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
21:06:48.424 INFO AddFlowSNVQuality - Shutting down engine
[June 12, 2025 at 9:06:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1920991232
21:06:48.538 INFO AddFlowSNVQuality - ------------------------------------------------------------
21:06:48.538 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:06:48.538 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
21:06:48.538 INFO AddFlowSNVQuality - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:06:48.538 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:06:48.538 INFO AddFlowSNVQuality - Start Date/Time: June 12, 2025 at 9:06:48 PM GMT
21:06:48.538 INFO AddFlowSNVQuality - ------------------------------------------------------------
21:06:48.538 INFO AddFlowSNVQuality - ------------------------------------------------------------
21:06:48.539 INFO AddFlowSNVQuality - HTSJDK Version: 4.2.0
21:06:48.539 INFO AddFlowSNVQuality - Picard Version: 3.4.0
21:06:48.539 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
21:06:48.539 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:06:48.539 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:06:48.539 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:06:48.539 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:06:48.539 INFO AddFlowSNVQuality - Deflater: IntelDeflater
21:06:48.539 INFO AddFlowSNVQuality - Inflater: IntelInflater
21:06:48.539 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
21:06:48.539 INFO AddFlowSNVQuality - Requester pays: disabled
21:06:48.539 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
21:06:48.539 INFO AddFlowSNVQuality - Initializing engine
21:06:48.598 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
21:06:48.600 INFO AddFlowSNVQuality - Done initializing engine
21:06:48.609 INFO ProgressMeter - Starting traversal
21:06:48.609 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
21:06:49.084 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
21:06:49.084 INFO ProgressMeter - chr1:14608 0.0 4278 540378.9
21:06:49.084 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
21:06:49.134 INFO AddFlowSNVQuality - Shutting down engine
[June 12, 2025 at 9:06:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1920991232