cluster() function only gives "unique" results

Hi, Pat and other mothur users,

I set cutoff=0.20 when I called dist.seqs(), and then called cluster() function without specifying the cutoff parameter. The problem is that in the result files (*.an.sabund, *an.rabund, *an.list), I only see a line for the “unique” results. I checked the logfile, it says “…changed cutoff to 0.002198…”. I also tried cluster() with cutoff=0.03, and I still only have unique line in the result files (and the mothur logfile now says “…changed cutoff to 0.001773…”).

I am using mothur v.1.19.4, 64 bit for linux.

Any help will be appreciated.


We commonly see this when people do not use screen.seqs to make sure that the sequences overlap and when people also do not use filter.seqs (w/ trump=.) to make sure the sequences overlap in the same alignment space. We also see it when the sequences are pretty distant from each other (e.g. protein coding DNA sequences).

Hope this helps,