Apparently not. It’s odd that the tax file I get from classify.otu has syntax errors for classify.tree.

Here’s what the logfile says:

mothur > classify.tree(taxonomy=hmw292c01Final.an.unique.cons.taxonomy, name=hmw292c01Final.names, group=hmw292c01Final.pick.groups, tree=hmw292c01Final.phylip.tre)

[ERROR]: OTU is missing the final ‘;’, ignoring.

[ERROR]: Taxonomy is missing the final ‘;’, ignoring.

[ERROR]: Otu00002 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Bacteroidetes”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00004 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);Betaproteobacteria(100);Rhodocyclales(100);Rhodocyclaceae(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00006 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00008 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);Alphaproteobacteria(100);Rhizobiales(100);Bradyrhizobiaceae(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00010 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00012 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);Betaproteobacteria(100);Rhodocyclales(100);Rhodocyclaceae(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00014 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00016 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00018 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);Gammaproteobacteria(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00020 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00022 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00024 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00026 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00028 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Bacteroidetes”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: 86 is already in your taxonomy file, names must be unique./n[ERROR]: Otu00030 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00032 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00034 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00036 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00038 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);Betaproteobacteria(100);Rhodocyclales(100);Rhodocyclaceae(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00040 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00042 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00044 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Bacteroidetes”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00046 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00048 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00050 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Bacteroidetes”(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00052 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp7(100);Acidobacteria_Gp7_order_incertae_sedis(100);Acidobacteria_Gp7_family_incertae_sedis(100);Gp7(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00054 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Acidobacteria”(100);Acidobacteria_Gp1(100);Acidobacteria_Gp1_order_incertae_sedis(100);Acidobacteria_Gp1_family_incertae_sedis(100);Gp1(100); is missing the final ‘;’, ignoring.

[ERROR]: Otu00056 is missing the final ‘;’, ignoring.

[ERROR]: Bacteria(100);“Proteobacteria”(100);Betaproteobacteria(100);unclassified(100);unclassified(100);unclassified(100); is missing the final ‘;’, ignoring.

[ERROR]: 54 is already in your taxonomy file, names must be unique./n

When I open the cons.taxonomy file everything looks okay to me.