Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
1.098s |
passed |
| testBasicBQ |
0.533s |
passed |
Standard error
20:51:52.551 INFO AddFlowSNVQuality - ------------------------------------------------------------
20:51:52.551 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
20:51:52.551 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
20:51:52.551 INFO AddFlowSNVQuality - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:51:52.551 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:51:52.551 INFO AddFlowSNVQuality - Start Date/Time: June 12, 2025 at 8:51:52 PM UTC
20:51:52.551 INFO AddFlowSNVQuality - ------------------------------------------------------------
20:51:52.551 INFO AddFlowSNVQuality - ------------------------------------------------------------
20:51:52.551 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:51:52.551 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:51:52.551 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:51:52.551 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:51:52.551 INFO AddFlowSNVQuality - Deflater: IntelDeflater
20:51:52.551 INFO AddFlowSNVQuality - Inflater: IntelInflater
20:51:52.551 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
20:51:52.551 INFO AddFlowSNVQuality - Requester pays: disabled
20:51:52.551 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
20:51:52.551 INFO AddFlowSNVQuality - Initializing engine
20:51:52.612 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
20:51:52.612 INFO AddFlowSNVQuality - Done initializing engine
20:51:52.624 INFO ProgressMeter - Starting traversal
20:51:52.624 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
20:51:53.508 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
20:51:53.508 INFO ProgressMeter - chr1:14608 0.0 4278 290362.0
20:51:53.508 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
20:51:53.559 INFO AddFlowSNVQuality - Shutting down engine
[June 12, 2025 at 8:51:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1902116864
20:51:53.648 INFO AddFlowSNVQuality - ------------------------------------------------------------
20:51:53.648 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
20:51:53.648 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
20:51:53.648 INFO AddFlowSNVQuality - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:51:53.648 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:51:53.648 INFO AddFlowSNVQuality - Start Date/Time: June 12, 2025 at 8:51:53 PM UTC
20:51:53.648 INFO AddFlowSNVQuality - ------------------------------------------------------------
20:51:53.648 INFO AddFlowSNVQuality - ------------------------------------------------------------
20:51:53.648 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:51:53.648 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:51:53.648 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:51:53.648 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:51:53.648 INFO AddFlowSNVQuality - Deflater: IntelDeflater
20:51:53.648 INFO AddFlowSNVQuality - Inflater: IntelInflater
20:51:53.648 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
20:51:53.648 INFO AddFlowSNVQuality - Requester pays: disabled
20:51:53.648 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
20:51:53.648 INFO AddFlowSNVQuality - Initializing engine
20:51:53.707 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
20:51:53.708 INFO AddFlowSNVQuality - Done initializing engine
20:51:53.717 INFO ProgressMeter - Starting traversal
20:51:53.717 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
20:51:54.040 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
20:51:54.040 INFO ProgressMeter - chr1:14608 0.0 4278 794674.9
20:51:54.040 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
20:51:54.090 INFO AddFlowSNVQuality - Shutting down engine
[June 12, 2025 at 8:51:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864