Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.974s |
passed |
| testBasicBQ |
0.565s |
passed |
Standard error
14:11:08.963 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:11:08.963 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:11:08.963 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
14:11:08.963 INFO AddFlowSNVQuality - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:11:08.963 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:11:08.963 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 2:11:08 PM GMT
14:11:08.963 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:11:08.963 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:11:08.964 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:11:08.964 INFO AddFlowSNVQuality - Picard Version: 3.4.0
14:11:08.964 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
14:11:08.964 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:11:08.964 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:11:08.964 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:11:08.964 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:11:08.964 INFO AddFlowSNVQuality - Deflater: IntelDeflater
14:11:08.964 INFO AddFlowSNVQuality - Inflater: IntelInflater
14:11:08.964 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
14:11:08.964 INFO AddFlowSNVQuality - Requester pays: disabled
14:11:08.964 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:11:08.964 INFO AddFlowSNVQuality - Initializing engine
14:11:09.023 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
14:11:09.024 INFO AddFlowSNVQuality - Done initializing engine
14:11:09.034 INFO ProgressMeter - Starting traversal
14:11:09.034 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:11:09.776 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
14:11:09.776 INFO ProgressMeter - chr1:14608 0.0 4278 345929.9
14:11:09.776 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
14:11:09.827 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 2:11:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1461714944
14:11:09.942 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:11:09.942 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:11:09.942 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
14:11:09.942 INFO AddFlowSNVQuality - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:11:09.942 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:11:09.942 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 2:11:09 PM GMT
14:11:09.942 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:11:09.942 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:11:09.942 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:11:09.942 INFO AddFlowSNVQuality - Picard Version: 3.4.0
14:11:09.942 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
14:11:09.942 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:11:09.942 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:11:09.942 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:11:09.942 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:11:09.942 INFO AddFlowSNVQuality - Deflater: IntelDeflater
14:11:09.942 INFO AddFlowSNVQuality - Inflater: IntelInflater
14:11:09.942 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
14:11:09.942 INFO AddFlowSNVQuality - Requester pays: disabled
14:11:09.942 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:11:09.942 INFO AddFlowSNVQuality - Initializing engine
14:11:10.007 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
14:11:10.008 INFO AddFlowSNVQuality - Done initializing engine
14:11:10.017 INFO ProgressMeter - Starting traversal
14:11:10.017 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:11:10.338 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
14:11:10.338 INFO ProgressMeter - chr1:14608 0.0 4278 799626.2
14:11:10.338 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
14:11:10.389 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 2:11:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1461714944