I’m using Mothur for microbiological analysis with PGM data. The tool is really awesome, and the SOP of Miseq helped a lot.
I used Mothur for several PGM project, and it turned out to be fine. But lately when I was analysing with “make.shared” command:
mothur > make.shared(list=abc.trim.unique.good.filter.unique.precluster.pick.an.list, group=abc.group, label=0.03)
The output just print “0.02” and resulting files contain no information of distance 0.03.
Afterwards, I tried to calculate the shannon index of distance 0.03, with command
mothur > collect.single(list=abc.trim.unique.good.filter.unique.precluster.pick.an.list, calc=shannon, label=0.03)
The output says “Your file does not include the label 0.03. I will use 0.02.”. Also no 0.03.
What the result was supposed to mean? Why was there no label of 0.03?
P.S. list file was generated by commands below:
mothur > dist.seqs(fasta=abc.trim.unique.good.filter.unique.precluster.pick.fasta, cutoff=0.10)
mothur > cluster(column=abc.trim.unique.good.filter.unique.precluster.pick.dist, name=abc.trim.unique.good.filter.unique.precluster.names, method=average)
Thanks in advance.