Possible memory leaks in minimap2-rs crate as nicely pulled apart by Rory:
jguhlin/minimap2-rs#40
Updating to new version with memory leak fix 0.1.15 from previous 0.1.14 and testing on leaky dataset run (SARS targeted sequencing in host background as control, 01:99). Still leaking heavily though...
Possible other cause: multiple basecaller servers running from failed runs? No.. still appears with only single runner
Possible other cause: dataset composition? No... still appears on the standard dataset (50:50 SARS)
Possible other cause: logging of mappings in debug mode - for some arcane reason this has messed up things in the past, but does not appear to be the case (removed from adaptive streaming service loop)
Possible other cause: location of reference index and reference index building? Here we go... if we load from SSD the minimap2-rs aligner is built fast (same time or slightly before data generation stream commences) - but loading it from HDD significantly delays this, which for some reason causes the memory leak
Possible memory leaks in
minimap2-rscrate as nicely pulled apart by Rory:jguhlin/minimap2-rs#40
Updating to new version with memory leak fix 0.1.15 from previous 0.1.14 and testing on leaky dataset run (SARS targeted sequencing in host background as control, 01:99). Still leaking heavily though...
Possible other cause: multiple
basecallerservers running from failed runs? No.. still appears with only single runnerPossible other cause: dataset composition? No... still appears on the standard dataset (50:50 SARS)
Possible other cause: logging of mappings in debug mode - for some arcane reason this has messed up things in the past, but does not appear to be the case (removed from adaptive streaming service loop)
Possible other cause: location of reference index and reference index building? Here we go... if we load from SSD the
minimap2-rsaligner is built fast (same time or slightly before data generation stream commences) - but loading it from HDD significantly delays this, which for some reason causes the memory leak