many files output in clasiify.otu command

Commands in mothur
1

Hi Everyone,
I ran the classify.otu(list=…/final.an.list, name=…/names.final, taxonomy=…/demultiplexed.unique.filter.unique.pick.rdp.taxonomy) command and I am getting this output.
Output File Names:
…/final.an.uniquecons.taxonomy
…/final.an.uniquecons.tax.summary
…/final.an.0.01cons.taxonomy
…/final.an.0.01cons.tax.summary
…/final.an.0.02cons.taxonomy
…/final.an.0.02cons.tax.summary
…/final.an.0.03cons.taxonomy
…/final.an.0.03cons.tax.summary
…/final.an.0.04cons.taxonomy
…/final.an.0.04cons.tax.summary
…/final.an.0.05cons.taxonomy
…/final.an.0.05cons.tax.summary
…/final.an.0.06cons.taxonomy
…/final.an.0.06cons.tax.summary
…/final.an.0.07cons.taxonomy
…/final.an.0.07cons.tax.summary
…/final.an.0.08cons.taxonomy
…/final.an.0.08cons.tax.summary
…/final.an.0.09cons.taxonomy
…/final.an.0.09cons.tax.summary
and many more.
I am wondering if we should get many files or only few.
My final.an.uniquecons.taxonomy looks like this:
Otu7714 1 Bacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Streptococcaceae(100);Streptococcus(100);unclassified(100);unclassified(100);
Otu7715 1 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu7716 1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu7717 1 Bacteria(100);Verrucomicrobia(100);Subdivision3(100);Subdivision3_genera_incertae_sedis(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu7718 1 Bacteria(100);Bacteroidetes(100);Sphingobacteria(100);Sphingobacteriales(100);Chitinophagaceae(100);unclassified(100);unclassified(100);unclassified(100);
Otu7719 1 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);unclassified(100);unclassified(100);


It has 7719 OTUs which is the same number of sequences I put.

I am not understanding it, please can anyone explain me.
Thanks!!!

2

By default it mothur will produce an output for each OTU resolution given in your list file (unique, then 1% increments up to the maximum). If you want to just specify a particular OTU threshold add the label parameter, eg:

classify.otu(list=…/final.an.list, name=…/names.final, taxonomy=…/demultiplexed.unique.filter.unique.pick.rdp.taxonomy, label=0.03)

This is true for quite a few of the commands, such as make.shared(), tree.shared() etc.

EDIT:
Unique OTUs are essentially the unique sequences in your data set. Depending on your data, it could be that the unique OTUs are equal to the total number of sequences, although I’d be suspicious of it if it isn’t an in silico experiment. Have you tried to dereplicate your data using unique.seqs()?

3

Thanks dwaite,
I did dereplicate my data using uinque…seqs(), and all the sequences I have are all unique, so I have 7719 unique sequences. When I used label=0.03, I got only two files as output.
Thanks!!!