Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
1.185s |
passed |
| testBasicBQ |
0.757s |
passed |
Standard error
18:38:32.677 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:38:32.677 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:38:32.677 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
18:38:32.677 INFO AddFlowSNVQuality - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:38:32.677 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:38:32.677 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 6:38:32 PM GMT
18:38:32.677 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:38:32.677 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:38:32.678 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:38:32.678 INFO AddFlowSNVQuality - Picard Version: 3.4.0
18:38:32.678 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
18:38:32.678 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:38:32.678 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:38:32.678 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:38:32.678 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:38:32.678 INFO AddFlowSNVQuality - Deflater: IntelDeflater
18:38:32.678 INFO AddFlowSNVQuality - Inflater: IntelInflater
18:38:32.678 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
18:38:32.678 INFO AddFlowSNVQuality - Requester pays: disabled
18:38:32.678 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:38:32.678 INFO AddFlowSNVQuality - Initializing engine
18:38:32.742 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
18:38:32.744 INFO AddFlowSNVQuality - Done initializing engine
18:38:32.759 INFO ProgressMeter - Starting traversal
18:38:32.760 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:38:33.672 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
18:38:33.672 INFO ProgressMeter - chr1:14608 0.0 4278 281447.4
18:38:33.672 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
18:38:33.722 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 6:38:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1478492160
18:38:33.872 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:38:33.872 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:38:33.872 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
18:38:33.872 INFO AddFlowSNVQuality - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:38:33.872 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:38:33.872 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 6:38:33 PM GMT
18:38:33.872 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:38:33.872 INFO AddFlowSNVQuality - ------------------------------------------------------------
18:38:33.873 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:38:33.873 INFO AddFlowSNVQuality - Picard Version: 3.4.0
18:38:33.873 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
18:38:33.873 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:38:33.873 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:38:33.873 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:38:33.873 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:38:33.873 INFO AddFlowSNVQuality - Deflater: IntelDeflater
18:38:33.873 INFO AddFlowSNVQuality - Inflater: IntelInflater
18:38:33.873 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
18:38:33.873 INFO AddFlowSNVQuality - Requester pays: disabled
18:38:33.873 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:38:33.873 INFO AddFlowSNVQuality - Initializing engine
18:38:33.938 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
18:38:33.940 INFO AddFlowSNVQuality - Done initializing engine
18:38:33.951 INFO ProgressMeter - Starting traversal
18:38:33.951 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
18:38:34.426 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
18:38:34.426 INFO ProgressMeter - chr1:14608 0.0 4278 540378.9
18:38:34.426 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
18:38:34.476 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 6:38:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160