A couple of issues here. What I run is this:
cluster(column=thesis.dist, name=thesis.names, cutoff=0.03, hard=t)
And it puts out:
1 0 etc…
changed cutoff to 0.0559848
So it seems like hard=t is not working.
Next issue, when I run:
bin.seqs(list=thesis.tx.list, fasta=thesis.fasta, name=thesis.names, label=0.03)
Your file does not include the label
0.03. I will use the next smallest distance.
Output File Names:
So I cannot retrieve OTUs at a specified cut-off, 0.05 doesn’t work either.