Steven Salzberg

this should only take a minute to classify. You might have enough RAM but your OS might be set so that you can only use 50% of it for 1...

if the hosts have 128 Gb then I recommend you use a size much smaller than that, not 120G, when running KrakenUniq. Try it with 32G and see if that...

I see what's happening now. You are running out of temp storage space. In order to run in less RAM, krakenuniq with the preload-size option goes through the database in...

hi @pfeiferd, that simply should not happen: kraken1 and krakenuniq should have identical k-mer counts, as long as you used the same database. I looked it up and I see...

I'm afraid I don't have time to debug this myself. I will ask a person in my lab about it, but it might take some time. It is possible that...

Yes, we do plan to update them, but they are huge, so this won't happen as often. We have several smaller ones, more specialized, so we might try to add...

Don't use --preload, but instead use --preload-size (this applies to @biolougy's question above). We probably should just deprecate the --preload option because the newer preload-size is just better. --preload still...

I don't recommend such a large value for preload-size (80GB). Then it has to write a large file to your hard disk, which you say is slow. Use 20GB instead...

not for download - but you can always make your own DB. Note that the new low-memory option means you can use the full DB, even the one over 400GB...

You can run KrakenUniq instead using any size DB you want, with a --preload-size option. We published this in bioRxiv and an open CS journal: https://joss.theoj.org/papers/10.21105/joss.04908 However note that KrakenUniq...