Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.942s |
passed |
| testBasicBQ |
0.633s |
passed |
Standard error
19:05:21.761 INFO AddFlowSNVQuality - ------------------------------------------------------------
19:05:21.761 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
19:05:21.761 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
19:05:21.761 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:05:21.761 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:05:21.761 INFO AddFlowSNVQuality - Start Date/Time: May 19, 2025 at 7:05:21 PM UTC
19:05:21.761 INFO AddFlowSNVQuality - ------------------------------------------------------------
19:05:21.761 INFO AddFlowSNVQuality - ------------------------------------------------------------
19:05:21.761 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:05:21.761 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:05:21.761 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:05:21.761 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:05:21.761 INFO AddFlowSNVQuality - Deflater: IntelDeflater
19:05:21.761 INFO AddFlowSNVQuality - Inflater: IntelInflater
19:05:21.761 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
19:05:21.761 INFO AddFlowSNVQuality - Requester pays: disabled
19:05:21.761 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:05:21.761 INFO AddFlowSNVQuality - Initializing engine
19:05:21.820 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
19:05:21.821 INFO AddFlowSNVQuality - Done initializing engine
19:05:21.836 INFO ProgressMeter - Starting traversal
19:05:21.836 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
19:05:22.572 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
19:05:22.572 INFO ProgressMeter - chr1:14608 0.0 4278 348750.0
19:05:22.572 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
19:05:22.622 INFO AddFlowSNVQuality - Shutting down engine
[May 19, 2025 at 7:05:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1761607680
19:05:22.713 INFO AddFlowSNVQuality - ------------------------------------------------------------
19:05:22.713 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
19:05:22.713 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
19:05:22.713 INFO AddFlowSNVQuality - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:05:22.713 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:05:22.713 INFO AddFlowSNVQuality - Start Date/Time: May 19, 2025 at 7:05:22 PM UTC
19:05:22.713 INFO AddFlowSNVQuality - ------------------------------------------------------------
19:05:22.713 INFO AddFlowSNVQuality - ------------------------------------------------------------
19:05:22.713 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:05:22.713 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:05:22.713 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:05:22.713 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:05:22.713 INFO AddFlowSNVQuality - Deflater: IntelDeflater
19:05:22.713 INFO AddFlowSNVQuality - Inflater: IntelInflater
19:05:22.713 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
19:05:22.713 INFO AddFlowSNVQuality - Requester pays: disabled
19:05:22.713 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:05:22.713 INFO AddFlowSNVQuality - Initializing engine
19:05:22.773 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
19:05:22.774 INFO AddFlowSNVQuality - Done initializing engine
19:05:22.783 INFO ProgressMeter - Starting traversal
19:05:22.783 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
19:05:23.199 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
19:05:23.200 INFO ProgressMeter - chr1:14608 0.0 4278 617019.2
19:05:23.200 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
19:05:23.250 INFO AddFlowSNVQuality - Shutting down engine
[May 19, 2025 at 7:05:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1761607680