Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.859s |
passed |
| testBasicBQ |
0.618s |
passed |
Standard error
15:03:25.911 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:03:25.911 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
15:03:25.911 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
15:03:25.911 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:03:25.911 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:03:25.911 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 3:03:25 PM UTC
15:03:25.911 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:03:25.911 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:03:25.911 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:03:25.911 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:03:25.911 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:03:25.911 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:03:25.911 INFO AddFlowSNVQuality - Deflater: IntelDeflater
15:03:25.911 INFO AddFlowSNVQuality - Inflater: IntelInflater
15:03:25.911 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
15:03:25.911 INFO AddFlowSNVQuality - Requester pays: disabled
15:03:25.911 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:03:25.911 INFO AddFlowSNVQuality - Initializing engine
15:03:25.969 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
15:03:25.970 INFO AddFlowSNVQuality - Done initializing engine
15:03:25.978 INFO ProgressMeter - Starting traversal
15:03:25.978 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:03:26.642 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
15:03:26.642 INFO ProgressMeter - chr1:14608 0.0 4278 386566.3
15:03:26.642 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
15:03:26.692 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 3:03:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
15:03:26.778 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:03:26.778 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
15:03:26.778 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
15:03:26.778 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:03:26.778 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:03:26.778 INFO AddFlowSNVQuality - Start Date/Time: May 27, 2025 at 3:03:26 PM UTC
15:03:26.778 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:03:26.778 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:03:26.778 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:03:26.778 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:03:26.778 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:03:26.778 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:03:26.778 INFO AddFlowSNVQuality - Deflater: IntelDeflater
15:03:26.778 INFO AddFlowSNVQuality - Inflater: IntelInflater
15:03:26.778 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
15:03:26.778 INFO AddFlowSNVQuality - Requester pays: disabled
15:03:26.778 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:03:26.778 INFO AddFlowSNVQuality - Initializing engine
15:03:26.835 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
15:03:26.836 INFO AddFlowSNVQuality - Done initializing engine
15:03:26.844 INFO ProgressMeter - Starting traversal
15:03:26.844 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:03:27.248 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
15:03:27.248 INFO ProgressMeter - chr1:14608 0.0 4278 635346.5
15:03:27.248 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
15:03:27.298 INFO AddFlowSNVQuality - Shutting down engine
[May 27, 2025 at 3:03:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864