Trouble including a taxonomy file in make.biom

mothur bugs
1

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.

2

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

3

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

4

Brilliant! Thanks a lot.