Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.819s |
passed |
| testBasicBQ |
0.653s |
passed |
Standard error
15:50:37.167 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:50:37.167 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
15:50:37.167 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
15:50:37.167 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:50:37.167 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:50:37.167 INFO AddFlowSNVQuality - Start Date/Time: May 19, 2025 at 3:50:37 PM UTC
15:50:37.167 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:50:37.167 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:50:37.167 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:50:37.167 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:50:37.167 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:50:37.167 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:50:37.167 INFO AddFlowSNVQuality - Deflater: IntelDeflater
15:50:37.167 INFO AddFlowSNVQuality - Inflater: IntelInflater
15:50:37.167 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
15:50:37.167 INFO AddFlowSNVQuality - Requester pays: disabled
15:50:37.167 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:50:37.167 INFO AddFlowSNVQuality - Initializing engine
15:50:37.227 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
15:50:37.228 INFO AddFlowSNVQuality - Done initializing engine
15:50:37.239 INFO ProgressMeter - Starting traversal
15:50:37.239 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:50:37.847 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
15:50:37.847 INFO ProgressMeter - chr1:14608 0.0 4278 422171.1
15:50:37.847 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
15:50:37.897 INFO AddFlowSNVQuality - Shutting down engine
[May 19, 2025 at 3:50:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
15:50:37.987 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:50:37.987 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
15:50:37.987 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
15:50:37.987 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:50:37.987 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:50:37.987 INFO AddFlowSNVQuality - Start Date/Time: May 19, 2025 at 3:50:37 PM UTC
15:50:37.987 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:50:37.987 INFO AddFlowSNVQuality - ------------------------------------------------------------
15:50:37.987 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:50:37.987 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:50:37.987 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:50:37.987 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:50:37.987 INFO AddFlowSNVQuality - Deflater: IntelDeflater
15:50:37.987 INFO AddFlowSNVQuality - Inflater: IntelInflater
15:50:37.987 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
15:50:37.987 INFO AddFlowSNVQuality - Requester pays: disabled
15:50:37.987 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:50:37.987 INFO AddFlowSNVQuality - Initializing engine
15:50:38.053 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
15:50:38.054 INFO AddFlowSNVQuality - Done initializing engine
15:50:38.063 INFO ProgressMeter - Starting traversal
15:50:38.064 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:50:38.498 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
15:50:38.498 INFO ProgressMeter - chr1:14608 0.0 4278 591428.6
15:50:38.498 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
15:50:38.548 INFO AddFlowSNVQuality - Shutting down engine
[May 19, 2025 at 3:50:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864