EggNOG-mapper online version vs command line version have different outputs

[bongoholmk]

Hello. I am using EggNOG-mapper to functionally annotate my genome of an African antelope ~2.9Gb. I used GeMoMa to structurally annotate using 6 different species. GeMoMa produced 29820 gene models and 55745 predicted proteins. I used the predicted proteins fasta file for EggNOG both the online version and the command line version and got very different outputs. I counted the unique orthologs in each output using R: online (29000, xlsx file) and command line (12900). All parameters were the same in both forms of EggNOG.

I am not sure how to interpret the results and which column to use to count unique orthologs. Why are they so different? I would also like to perform a gene ontology enrichment analysis. How or what would you recommend for this analysis?

Thank you for your time,
Karen