So I have been following the Costello Stool Analysis on the website but for some reason, I cannot cluster at anything less than .10 level, even though I am expecting very similar sequences. I have done exactly the same steps except I excluded the chimera.slayer step. Is there a reason behind this?
Are you using the Costello sequences? If not, have you tried to replicate what we did with those sequences and gotten it to work? Could you email us a copy of the mothur.*.logfile (firstname.lastname@example.org)?
The reason you are unable to cluster below 0.10 is that the smallest distance in your distance file is 0.10. Some of your distances are pretty large (up to 1.00). This typically indicates alignment problems. Your sequences really should overlap over the same region.
I noticed you are running version 1.7. We have added many new features as well as updated many commands to help catch some common problems since then. You may want to consider upgrading to 1.11.0.
Hope this helps!