I am clustering 112453 unique sequences using cluster comment in mothur. I used following comments,
cluster(column=soil_leaf_root_16s.trim.unique.good.filter.unique.precluster.pick.pick.dist, name=soil_leaf_root_16s.trim.unique.good.filter.unique.precluster.pick.pick.names, cutoff=0.03).
I got a list file for only unique sequences and there is also no output files in mothur yet. Do you think still i need to wait to get other cutoff level or could be any problem? Kindly let me know! Thanks.

Cutoff needs to be set higher than the desired OTU level. For example I’m generally interested in 0.03, 0.05, and 0.1 OTUs so I set my cutoff at 0.15. Since I use cluster split there are groups that don’t have any seqs that are greater than 0.15 apart so I’ll get a message saying the the cutoff was changed to a smaller value.

Here’s an explanation of what’s going on…