get.communitytype usable with processors=1?

Trying out get.communitytype on a single MiSeq run, and since processors=1 is forced I’ve been wondering about the potential run time? Is the command still viable like this?

Had it running for 6+ hours now and it hasn’t gone through a single K pass yet, or at least there is no output…

mothur > get.communitytype(, processors=48)
Using 1 processor
K       NLE             logDet  BIC             AIC             Laplace


Just to confirm that it takes rather long. It’s been running now for 2 days:

K       NLE             logDet  BIC             AIC             Laplace
1       385260.41       10029.11        420354.81       400897.41       375905.53
2       415038.96       -18163.15       485230.01       446313.96       377217.60

You might want to try it with genus-level phylotype data rather than OTUs. I suspect you may not find any types using OTUs because the distributions will be so flat.

It finished after a few more days but as you said, everything gets put in one type while with previous clustering methods I was getting consistently (in my case) 4 groups :confused:

Thanks for the tip, I will give it a try.