Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
1.059s |
passed |
| testBasicBQ |
0.626s |
passed |
Standard error
14:41:56.800 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:41:56.800 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:41:56.800 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
14:41:56.800 INFO AddFlowSNVQuality - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:41:56.800 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:41:56.800 INFO AddFlowSNVQuality - Start Date/Time: June 2, 2025 at 2:41:56 PM GMT
14:41:56.800 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:41:56.800 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:41:56.801 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:41:56.801 INFO AddFlowSNVQuality - Picard Version: 3.4.0
14:41:56.801 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
14:41:56.801 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:41:56.801 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:41:56.801 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:41:56.801 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:41:56.801 INFO AddFlowSNVQuality - Deflater: IntelDeflater
14:41:56.801 INFO AddFlowSNVQuality - Inflater: IntelInflater
14:41:56.801 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
14:41:56.801 INFO AddFlowSNVQuality - Requester pays: disabled
14:41:56.801 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:41:56.801 INFO AddFlowSNVQuality - Initializing engine
14:41:56.864 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
14:41:56.865 INFO AddFlowSNVQuality - Done initializing engine
14:41:56.876 INFO ProgressMeter - Starting traversal
14:41:56.876 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:41:57.694 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
14:41:57.694 INFO ProgressMeter - chr1:14608 0.0 4278 313789.7
14:41:57.694 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
14:41:57.745 INFO AddFlowSNVQuality - Shutting down engine
[June 2, 2025 at 2:41:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1757413376
14:41:57.861 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:41:57.861 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:41:57.861 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
14:41:57.861 INFO AddFlowSNVQuality - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:41:57.861 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:41:57.861 INFO AddFlowSNVQuality - Start Date/Time: June 2, 2025 at 2:41:57 PM GMT
14:41:57.861 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:41:57.861 INFO AddFlowSNVQuality - ------------------------------------------------------------
14:41:57.861 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:41:57.861 INFO AddFlowSNVQuality - Picard Version: 3.4.0
14:41:57.861 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
14:41:57.861 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:41:57.861 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:41:57.861 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:41:57.861 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:41:57.861 INFO AddFlowSNVQuality - Deflater: IntelDeflater
14:41:57.861 INFO AddFlowSNVQuality - Inflater: IntelInflater
14:41:57.861 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
14:41:57.861 INFO AddFlowSNVQuality - Requester pays: disabled
14:41:57.861 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:41:57.861 INFO AddFlowSNVQuality - Initializing engine
14:41:57.920 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
14:41:57.921 INFO AddFlowSNVQuality - Done initializing engine
14:41:57.929 INFO ProgressMeter - Starting traversal
14:41:57.930 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:41:58.314 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
14:41:58.314 INFO ProgressMeter - chr1:14608 0.0 4278 668437.5
14:41:58.314 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
14:41:58.364 INFO AddFlowSNVQuality - Shutting down engine
[June 2, 2025 at 2:41:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1757413376