Best homology group in eggnog-mapper 2.0.1

Question

[Asaf]

Hi,

I'm trying to annotate a meta-genome assembly. I used eggnog-mapper version 2.0.1 which apparently only allow diamond mapping, hmmer based mapping is deprecated. The output annotations file contain a list of possible homology groups but it doesn't give the best OG. The documentation says that the best OG will only be given when using hmmer. Any idea how to get this data? Thanks

Here is an output line for example:

#query_name     seed_eggNOG_ortholog    seed_ortholog_evalue    seed_ortholog_score     best_tax_level Preferred_name  GOs     EC      KEGG_ko KEGG_Pathway    KEGG_Module    KEGG_Reaction   KEGG_rclass     BRITE   KEGG_TC CAZy    BiGG_Reaction   taxonomic scope eggNOG OGs      best eggNOG OG  COG Functional cat.     eggNOG free text desc.
AONAOMJJ_00001  1235796.C815_00390      4.6e-158        564.3   Firmicutes      capA                    ko:K07282                                       ko00000       Bacteria 1UCFI@1239,COG2843@1,COG2843@2  NA|NA|NA        M       enzyme of poly-gamma-glutamate biosynthesis (Capsule formation)

[xonq]

just ranting, but why is hmmer still the default option then let alone even listed in the arguments. I get a lot of headaches from trying emapper

[F.Bedjou]

were you able to get these desired results with eggnog? I'm stuck on it

Answer 1

[Asaf]

Okay, so after doing some digging, indeed the hmmer option is dead in V2 and diamond should be used also for previous versions. The list of OGs contains orthology groups from different taxonomic levels, having the taxid after the "@" so in the example above 1UCFI@1239,COG2843@1,COG2843@2 means there are OGs in the Firmicutes, root and Bacteria.