Trouble including a taxonomy file in make.biom

Hi,

I’ve been trying to use the make.biom() command to convert my shared file into a biom file. It works fine, but if I try to add a taxonomy file it gives me an error. The exact commands I’m running are (I have the standard fasta, names, groups, and taxonomy files as per the SOP):

mothur > dist.seqs(fasta=final.fasta, cutoff=0.15)
mothur > cluster(column=current, name=final.names)
mothur > get.oturep(list=current, fasta=current, name=current, column=current, label=0.03)
mothur > classify.otu(list=current, name=current, taxonomy=final.pds.taxonomy, label=0.03)
mothur > make.shared(list=current, group=final.groups, label=0.03)
mothur > make.biom(shared=current, contaxonomy=final.an.0.03cons.taxonomy)

Which gives me an error “[ERROR]: can’t find taxonomy information for Otu001”. If I open the cons.taxonomy file, the first two lines are:

OTU Size Taxonomy
Otu001 14 Bacteria(100);Firmicutes(100);Bacilli(100);Bacillales(100);Bacillaceae_1(100);Aeribacillus(100);

And in the shared file the first four columns are labelled "label Group numOtus Otu001". Is this a real bug, or am I missing something simple?

Thanks for your help.

Hi there,

I was having the same issue and tracked down the problem:

Using mothur-v1.27, if you look at the consensus taxonomy file produced using classify.otu the file looks something like this:

OTU Size Taxonomy
Otu0001 1 Bacteria(100);TM7(100);TM7-3(100);CW040(100);F16(100);otu_4381(100);unclassified(100);unclassified(100);
Otu0002 1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu0003 2 Bacteria(100);Fusobacteria(100);Fusobacteria_(class)(100);Fusobacteriales(100);Fusobacteriaceae(100);Sneathia(100);Leptotrichia_amnionii(100);otu_2301(100);

However, the example files for the consensus taxonomy on the website look like this (final.tx.1.cons.taxonomy):
OTU Size Taxonomy
1 29357 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);“Porphyromonadaceae”(100);unclassified(100);
2 2223 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);“Rikenellaceae”(100);Alistipes(100);
3 3211 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);unclassified(100);unclassified(100);
4 4646 Bacteria(100);“Firmicutes”(100);“Clostridia”(100);Clostridiales(100);unclassified(100);unclassified(100);

The problem seems to be that mothur isn’t expecting the Otu0001 in the consensus taxonomy file, and instead wants either 1 or 0001 for the first OTU.

So, an easy work-around is this: If you just open your consensus taxonomy file in a text editor and remove all leading Otu labels (e.g. Otu0001, Otu0002, Otu0003 change to 0001, 0002, 0003 or 1, 2, 3) and re-run make.biom it works just fine with the corrected consensus taxonomy file.

Hope that helps!

Best,
Emiley

You are exactly right, Emiley. This will be fixed in our next release.

Brilliant! Thanks a lot.