Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.956s |
passed |
| testBasicBQ |
0.613s |
passed |
Standard error
22:50:35.310 INFO AddFlowSNVQuality - ------------------------------------------------------------
22:50:35.310 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
22:50:35.310 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
22:50:35.310 INFO AddFlowSNVQuality - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:50:35.310 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:50:35.310 INFO AddFlowSNVQuality - Start Date/Time: March 28, 2025 at 10:50:35 PM UTC
22:50:35.310 INFO AddFlowSNVQuality - ------------------------------------------------------------
22:50:35.310 INFO AddFlowSNVQuality - ------------------------------------------------------------
22:50:35.310 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:50:35.310 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:50:35.311 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:50:35.311 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:50:35.311 INFO AddFlowSNVQuality - Deflater: IntelDeflater
22:50:35.311 INFO AddFlowSNVQuality - Inflater: IntelInflater
22:50:35.311 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
22:50:35.311 INFO AddFlowSNVQuality - Requester pays: disabled
22:50:35.311 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
22:50:35.311 INFO AddFlowSNVQuality - Initializing engine
22:50:35.367 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
22:50:35.368 INFO AddFlowSNVQuality - Done initializing engine
22:50:35.377 INFO ProgressMeter - Starting traversal
22:50:35.377 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
22:50:36.120 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
22:50:36.120 INFO ProgressMeter - chr1:14608 0.0 4278 345464.3
22:50:36.120 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
22:50:36.170 INFO AddFlowSNVQuality - Shutting down engine
[March 28, 2025 at 10:50:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1447034880
22:50:36.260 INFO AddFlowSNVQuality - ------------------------------------------------------------
22:50:36.260 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
22:50:36.260 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
22:50:36.260 INFO AddFlowSNVQuality - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:50:36.260 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:50:36.260 INFO AddFlowSNVQuality - Start Date/Time: March 28, 2025 at 10:50:36 PM UTC
22:50:36.260 INFO AddFlowSNVQuality - ------------------------------------------------------------
22:50:36.260 INFO AddFlowSNVQuality - ------------------------------------------------------------
22:50:36.260 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:50:36.260 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:50:36.260 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:50:36.260 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:50:36.260 INFO AddFlowSNVQuality - Deflater: IntelDeflater
22:50:36.261 INFO AddFlowSNVQuality - Inflater: IntelInflater
22:50:36.261 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
22:50:36.261 INFO AddFlowSNVQuality - Requester pays: disabled
22:50:36.261 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
22:50:36.261 INFO AddFlowSNVQuality - Initializing engine
22:50:36.325 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
22:50:36.326 INFO AddFlowSNVQuality - Done initializing engine
22:50:36.334 INFO ProgressMeter - Starting traversal
22:50:36.334 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
22:50:36.727 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
22:50:36.727 INFO ProgressMeter - chr1:14608 0.0 4278 653129.8
22:50:36.727 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
22:50:36.777 INFO AddFlowSNVQuality - Shutting down engine
[March 28, 2025 at 10:50:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1447034880