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AuReMe / emapper2gbk

Convert GFF, fastas, annotation table and species name into Genbank.
GNU Lesser General Public License v3.0
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Question about new eggNOG output #14

Closed dzolier closed 2 years ago

dzolier commented 2 years ago

Hello, I'm trying to use Metage2Metabo with eggNOG output and MAG bins from metaWRAP, but I didn't get a .faa file when running eggNOG. It appears that eggNOG v2 no longer needs to make a .faa file in order to annotate bins.

I'm curious, is there a way I can use those two outputs -- metaWRAP && eggNOG -- without those .faa files? And if not, is there an alternative method of creating a .faa file?

Thank you for your help.

ArnaudBelcour commented 2 years ago

Hi @dzolier,

So you give fastas containing the nucleic sequences of the genomes to eggNOG and it gives you the annotation but not the amino-acids sequences associated with them? It is strange, because with the version that I have tested, I always get amino-acids sequences (output files with name ending with .emapper.genepred.fasta). EggNOG did not produced any of these files? Which versions among the v2 version of eggNOG do you use?

I could check to see if there is a possibility to put the faa file as optional but this will require to make some test with Pathway Tools to ensure that this causes no issue and I do not have a lot of time right now to test this.

Best regards, Arnaud Belcour.

dzolier commented 2 years ago

I must have just gotten a weird run. I tried it again and everything worked like a charm. Thanks!