Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
1.097s |
passed |
| testBasicBQ |
0.755s |
passed |
Standard error
16:56:05.797 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:56:05.797 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:56:05.797 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
16:56:05.798 INFO AddFlowSNVQuality - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:56:05.798 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:56:05.798 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 4:56:05 PM GMT
16:56:05.798 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:56:05.798 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:56:05.798 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:56:05.798 INFO AddFlowSNVQuality - Picard Version: 3.4.0
16:56:05.798 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
16:56:05.798 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:56:05.798 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:56:05.798 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:56:05.798 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:56:05.798 INFO AddFlowSNVQuality - Deflater: IntelDeflater
16:56:05.798 INFO AddFlowSNVQuality - Inflater: IntelInflater
16:56:05.798 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
16:56:05.798 INFO AddFlowSNVQuality - Requester pays: disabled
16:56:05.798 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:56:05.798 INFO AddFlowSNVQuality - Initializing engine
16:56:05.857 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
16:56:05.858 INFO AddFlowSNVQuality - Done initializing engine
16:56:05.867 INFO ProgressMeter - Starting traversal
16:56:05.867 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:56:06.729 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
16:56:06.729 INFO ProgressMeter - chr1:14608 0.0 4278 297772.6
16:56:06.729 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
16:56:06.780 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 4:56:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1956642816
16:56:06.899 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:56:06.900 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:56:06.900 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
16:56:06.900 INFO AddFlowSNVQuality - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:56:06.900 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:56:06.900 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 4:56:06 PM GMT
16:56:06.900 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:56:06.900 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:56:06.900 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:56:06.900 INFO AddFlowSNVQuality - Picard Version: 3.4.0
16:56:06.900 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
16:56:06.900 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:56:06.900 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:56:06.900 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:56:06.900 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:56:06.900 INFO AddFlowSNVQuality - Deflater: IntelDeflater
16:56:06.900 INFO AddFlowSNVQuality - Inflater: IntelInflater
16:56:06.900 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
16:56:06.900 INFO AddFlowSNVQuality - Requester pays: disabled
16:56:06.900 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:56:06.900 INFO AddFlowSNVQuality - Initializing engine
16:56:06.959 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
16:56:06.960 INFO AddFlowSNVQuality - Done initializing engine
16:56:06.974 INFO ProgressMeter - Starting traversal
16:56:06.974 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:56:07.473 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
16:56:07.473 INFO ProgressMeter - chr1:14608 0.0 4278 514388.8
16:56:07.473 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
16:56:07.523 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 4:56:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1956642816