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(shared=run066_09122016.an.0.03.pick.0.03.subsample.shared, processors=48)
Using 1 processor
0.03
K NLE logDet BIC AIC Laplace
Thx.
Just to confirm that it takes rather long. It’s been running now for 2 days:
0.03
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 
Thanks for the tip, I will give it a try.