Jeff Brown

Ah good catch, it looks like there's some funny differences between MacOS and Linux versions of sed, specifically with implicit definitions of backup files (very well explained [on this stackoverflow...

This is an interesting issue, it appears that there are more than one publication online referencing "M00260" as "DNA polymerase III complex, bacteria"- but the KEGG database does not seem...

It looks like the KEGG module database was update late 2019 in release 92 [KEGG release notes](https://www.genome.jp/kegg/docs/relnote.html) where they removed some redundancies and reorganized. eggnog 5.0 was published late 2018,...

No problem :) I couldn't find any way to access previous versions of KEGG or KEGG modules, but others with more experience might know how to do so. I don't...

Hello, can you confirm whether you have downloaded the pfam database? It does not automatically donwload, and it is required for `--pfam_realign`. Based on your .log, you can run `ls...

@iferres I don't know if this helps, but the download_eggnog_data.py will only download the "baseline" eggNOG annotation database, the PFAM database is an optional download that is not included by...

Hello Karen, Could you post exactly what parameters you used for the standalone and online analyses? Could you also post the R script you used to count the unique orthologs...

can you run `head NGmerge_Results/Day049_D1_merged_1001.fq` and post the results here? What all was done on the sequences before running the .fq through eggnog? (trimming, assembly, etc.)