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I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the 'Orthogroup_Sequences' which contains a huge list of protein files in fasta format. As instructed, the folder was compressed into a tar.gz zip file and uploaded. If the upload was successful, an email is sent to your mail ID where you can check the details of your job and decide whether to START the job or not. Every time I START the job, it fails within a few minutes. Initially I presumed that it was due to the file size and hence reduced the number of sequences submitted, but in vain. Can anyone help me?

eggNOG-mapper : http://eggnog-mapper.embl.de/

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  • $\begingroup$ Which version of eggNOG-mapper is being used here? $\endgroup$
    – M__ ♦
    Commented Oct 4, 2023 at 12:01
  • $\begingroup$ Hi @M__ I think it's v2. That's what the citation says at the bottom of the page. it's probably v2.1.12. Do you think the command line version would be better? $\endgroup$
    – K_081
    Commented Oct 4, 2023 at 13:43

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There is a known bug between eggNOG-mapper2 and eggNOG6. This is described here: https://github.com/eggnogdb/eggnog-mapper/issues/428

In your case, I'm not sure on what strategy you are deploying after OrthoFinder, but there's a chance it's not solvable at present and the best place for information is the eggnog GitHub.

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    $\begingroup$ Thank you @M__ . I have posted my issue on the github page for failing eggNOG-mapper jobs. I have also tried to perform the same function using COGclassifer after concatenating all the .fa sequences in the Orthogroup_sequences file. Hopefully it yields reliable results. If you have any other suggestions please let me know. $\endgroup$
    – K_081
    Commented Oct 5, 2023 at 4:58
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    $\begingroup$ @K_081 Thanks it's a positive step forward. eggNOG is very, very good. I'm not be looking for a solution outside this. I'll keep an eye out for your GitHub post and I will be looking around for a way forward and post back here once done (timeline several weeks). $\endgroup$
    – M__ ♦
    Commented Oct 5, 2023 at 14:12
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    $\begingroup$ Hi @M__, I just got a reply on the github page from one of the developers I guess, and he has found an unwanted line in my file. It is the file created by OrthoFinder itself so I don't know how it appeared there. I'll have to check all the files before uploading them to eggNOG-mapper. $\endgroup$
    – K_081
    Commented Oct 5, 2023 at 15:52
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I'd like to answer my own question as I have found the solution for this and thought it might help anyone else trying to use eggNOG-mapper. The prerequisite for uploading the input file with the required collection of .faa files, is that, the file extension has to end with .gz. The site mentions that too. I had made the mistake of uploading a .tar.gz which is what my system produced as a compressed file of my folder of sequences. Although the upload was successful, the runs failed as the file had some unwanted lines owing to the .tar.gz format. I randomly uploaded a concatenated .faa file which worked well and got the results too! The trick is that, the input file has to be strictly a .gz and NOT .tar.gz or it could also be a .faa file with all the sequences.

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    $\begingroup$ Thanks for this that is very helpful. $\endgroup$
    – M__ ♦
    Commented Oct 15, 2023 at 12:30

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