Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.993s |
passed |
| testBasicBQ |
0.558s |
passed |
Standard error
15:18:15.191 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:18:15.191 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:18:15.191 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
15:18:15.191 INFO AddFlowSNVQuality - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:18:15.191 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:18:15.191 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 3:18:15 PM GMT
15:18:15.191 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:18:15.191 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:18:15.191 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:18:15.191 INFO AddFlowSNVQuality - Picard Version: 3.4.0
15:18:15.191 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
15:18:15.191 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:18:15.191 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:18:15.191 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:18:15.191 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:18:15.191 INFO AddFlowSNVQuality - Deflater: IntelDeflater
15:18:15.191 INFO AddFlowSNVQuality - Inflater: IntelInflater
15:18:15.191 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
15:18:15.191 INFO AddFlowSNVQuality - Requester pays: disabled
15:18:15.191 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:18:15.191 INFO AddFlowSNVQuality - Initializing engine
15:18:15.249 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
15:18:15.249 INFO AddFlowSNVQuality - Done initializing engine
15:18:15.264 INFO ProgressMeter - Starting traversal
15:18:15.264 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:18:16.026 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
15:18:16.026 INFO ProgressMeter - chr1:14608 0.0 4278 336850.4
15:18:16.026 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
15:18:16.076 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 3:18:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1841299456
15:18:16.186 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:18:16.186 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:18:16.186 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
15:18:16.186 INFO AddFlowSNVQuality - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:18:16.186 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:18:16.186 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 3:18:16 PM GMT
15:18:16.186 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:18:16.186 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:18:16.186 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:18:16.186 INFO AddFlowSNVQuality - Picard Version: 3.4.0
15:18:16.186 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
15:18:16.186 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:18:16.186 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:18:16.186 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:18:16.186 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:18:16.186 INFO AddFlowSNVQuality - Deflater: IntelDeflater
15:18:16.186 INFO AddFlowSNVQuality - Inflater: IntelInflater
15:18:16.186 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
15:18:16.186 INFO AddFlowSNVQuality - Requester pays: disabled
15:18:16.186 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:18:16.186 INFO AddFlowSNVQuality - Initializing engine
15:18:16.243 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
15:18:16.243 INFO AddFlowSNVQuality - Done initializing engine
15:18:16.252 INFO ProgressMeter - Starting traversal
15:18:16.252 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:18:16.580 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
15:18:16.580 INFO ProgressMeter - chr1:14608 0.0 4278 782561.0
15:18:16.580 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
15:18:16.630 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 3:18:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1841299456