Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.902s |
passed |
| testBasicBQ |
0.635s |
passed |
Standard error
16:08:00.161 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:08:00.161 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:08:00.161 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
16:08:00.161 INFO AddFlowSNVQuality - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:08:00.161 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:08:00.161 INFO AddFlowSNVQuality - Start Date/Time: May 19, 2025 at 4:08:00 PM GMT
16:08:00.161 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:08:00.161 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:08:00.161 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:08:00.161 INFO AddFlowSNVQuality - Picard Version: 3.4.0
16:08:00.161 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
16:08:00.161 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:08:00.161 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:08:00.161 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:08:00.161 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:08:00.161 INFO AddFlowSNVQuality - Deflater: IntelDeflater
16:08:00.161 INFO AddFlowSNVQuality - Inflater: IntelInflater
16:08:00.161 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
16:08:00.161 INFO AddFlowSNVQuality - Requester pays: disabled
16:08:00.161 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:08:00.161 INFO AddFlowSNVQuality - Initializing engine
16:08:00.225 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
16:08:00.227 INFO AddFlowSNVQuality - Done initializing engine
16:08:00.238 INFO ProgressMeter - Starting traversal
16:08:00.238 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:08:00.887 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
16:08:00.887 INFO ProgressMeter - chr1:14608 0.0 4278 395500.8
16:08:00.887 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
16:08:00.937 INFO AddFlowSNVQuality - Shutting down engine
[May 19, 2025 at 4:08:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1841299456
16:08:01.078 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:08:01.078 INFO AddFlowSNVQuality - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:08:01.078 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
16:08:01.078 INFO AddFlowSNVQuality - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:08:01.078 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:08:01.078 INFO AddFlowSNVQuality - Start Date/Time: May 19, 2025 at 4:08:01 PM GMT
16:08:01.078 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:08:01.078 INFO AddFlowSNVQuality - ------------------------------------------------------------
16:08:01.078 INFO AddFlowSNVQuality - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:08:01.078 INFO AddFlowSNVQuality - Picard Version: 3.4.0
16:08:01.078 INFO AddFlowSNVQuality - Built for Spark Version: 3.5.0
16:08:01.078 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:08:01.078 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:08:01.078 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:08:01.078 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:08:01.078 INFO AddFlowSNVQuality - Deflater: IntelDeflater
16:08:01.078 INFO AddFlowSNVQuality - Inflater: IntelInflater
16:08:01.078 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
16:08:01.078 INFO AddFlowSNVQuality - Requester pays: disabled
16:08:01.078 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:08:01.078 INFO AddFlowSNVQuality - Initializing engine
16:08:01.143 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
16:08:01.144 INFO AddFlowSNVQuality - Done initializing engine
16:08:01.154 INFO ProgressMeter - Starting traversal
16:08:01.154 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:08:01.514 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
16:08:01.514 INFO ProgressMeter - chr1:14608 0.0 4278 713000.0
16:08:01.514 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
16:08:01.565 INFO AddFlowSNVQuality - Shutting down engine
[May 19, 2025 at 4:08:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1841299456