Dada2 denoise-paired running time over 12 hours for 16 samples

Hi @Linevmo,
As you have seen discussed across the forum, runtime depends on many many things — see here. So other users' experiences may not extrapolate to your own.

If it is still running, it is still running — you will most likely get an error (e.g., a memory error) if it fails. 12 hours is not a long time for dada2 — even for a subset of samples if those samples have many sequences. I would recommend just waiting it out... 2-3 days of runtime are not unusual.

Sorry I don't have a more concrete response! I just recommend being a little more patient on this one...