# Trouble including a taxonomy file in make.biom **URL:** \ **Category:** mothur bugs\ **Created:** [October 1, 2012, 7:46pm UTC](https://forum.mothur.org/t/trouble-including-a-taxonomy-file-in-make-biom/1064 "2012-10-01T19:46:35Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![dwaite](https://avatars.discourse-cdn.com/v4/letter/d/ecccb3/32.png) [@dwaite](https://forum.mothur.org/u/dwaite)\ **Post date:** [October 1, 2012, 7:46pm UTC](https://forum.mothur.org/t/trouble-including-a-taxonomy-file-in-make-biom/1064/1 "2012-10-01T19:46:35Z")
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. ---
**Author:** ![eeloe](https://avatars.discourse-cdn.com/v4/letter/e/a698b9/32.png) [@eeloe](https://forum.mothur.org/u/eeloe)\ **Post date:** [October 12, 2012, 12:23pm UTC](https://forum.mothur.org/t/trouble-including-a-taxonomy-file-in-make-biom/1064/2 "2012-10-12T12:23:15Z")
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 ---
**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\ **Post date:** [October 12, 2012, 6:48pm UTC](https://forum.mothur.org/t/trouble-including-a-taxonomy-file-in-make-biom/1064/3 "2012-10-12T18:48:39Z")
You are exactly right, Emiley. This will be fixed in our next release. ---
**Author:** ![dwaite](https://avatars.discourse-cdn.com/v4/letter/d/ecccb3/32.png) [@dwaite](https://forum.mothur.org/u/dwaite)\ **Post date:** [October 14, 2012, 9:45pm UTC](https://forum.mothur.org/t/trouble-including-a-taxonomy-file-in-make-biom/1064/4 "2012-10-14T21:45:08Z")
Brilliant! Thanks a lot.