label not found in make.shared and collect.single

Commands in mothur
1

Hi, guys.
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.
TYF

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Anyone who can help?

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Here are some links you may find helpful:

http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F
http://www.mothur.org/wiki/Frequently_asked_questions#Why_is_data_missing_for_some_distance_levels.3F

It looks like the cluster command adjusted your cutoff to 0.02, and that’s why the list file does not contain 0.03. You might try increasing your cutoff.

4

westcott, thanks a lot.
I should have read FAQ first, such newbie questions.