Open ghost opened 4 years ago
Hi @aderzelle! The initial k-mer counting steps should be multithreaded, but the main procedure to identify novel k-mers is not multithreaded.
Hi @standage, thanks for a great tool which we've been working to integrate into our human disease trio work. We've hit an issue with the kevlar novel step though, which I think is similar to the issue @aderzelle raised. Basically, for some samples kevlar novel takes > 48h to complete. This is our HPC walltime limit, so effectively we can't process these samples with Kevlar right now. This is for ~40X human WGS.
Is there some way to parallelise the novel step, perhaps by splitting the case k-mer input? Alternatively can we tweak the config to improve speed without too much effect on sensitivity? Any ideas you have would be much appreciated, thanks!
Hello, I launched kevlar as such
It has been running for 10 hours now. But I never see more than 1 thread in use. Is it normal? Is this step not multithreaded? Thank you :)