COG, TIGRFAM "error - specified category is not one of the default categories."

[S. T.]

Dear Picrust2 developers,

First, thank you for this very efficient tool !

However, we are currently encountering some problems using the new version (v2.6) using conda. We did not observe any problems during the installation.

Then, we launched our analysis, and for some --in_traits options, we encountered this error message:

error - COG specified category is not one of the default categories. 

(for example for COG).

We then reinstall from the source (downloading it and following your recommandations). The pytest was OK, no error.

But, when we tried to relaunch the analysis again, same problem.

Is it because COG and TIGRFAM are not available in this version, or did we install something wrong ? Could you help us, at least for COG descriptions ?

Best regards,

Sebastien

[Robyn Wright]

Hi there,

You're correct, COG and TIGRFAM are not available in the latest version - I've used Eggnog for annotation instead and these aren't in the output there. There are several other types of functional annotation instead now (BiGG reaction, CAZy, gene names and GO annotations in addition to the EC number, KO and Pfam annotations that were available previously - all upper case if you're giving them to --in_traits: EC, KO, GO, PFAM, BIGG, CAZY, GENE_NAMES). You can see full details in our preprint. I have also just added instructions for creating a custom trait table for use with the new database, incase that is of interest to you (that's here). I'm currently making some edits to the Github so that hopefully it's a bit clearer what the options are for the current database. 

Best,

Robyn