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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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Is necessary download the databases "taxa database" and "diamond database" ? #292

Closed EulleSA closed 3 years ago

EulleSA commented 3 years ago

Hi, everybody!

I noticed that the "download_eggnog_data.py" script downloads 3 databases( annotation, taxa, and diamond).

Bearing in mind that I only want to perform the functional annotation to get the KO identifier of each annotated sequence, is it necessary to download all the databases?

Thanks in advance!

Cantalapiedra commented 3 years ago

Hi @EulleSA ,

You need the taxa database.

Regarding the diamond database, if your sequences are not eggnog proteins, or you don't have hits to eggnog proteins, you need to perform a search step, either with diamonds, mmseqs2 or hmmer. Diamond is the default, and that is why it is downloaded by default also.

I hope this makes sense.

Best, Carlos

EulleSA commented 3 years ago

I got it! Thank you very much, Catalapiedra!

EulleSA commented 3 years ago

@Cantalapiedra Could you tell me if you can define by command line to download all the necessary banks, without having to choose "y" and "n"?

Cantalapiedra commented 3 years ago

Hi @EulleSA ,

check download_eggnog_data.py --help. You should be able to do it with -D, -M, -H -d, -f, ...

Best, Carlos

EulleSA commented 3 years ago

Thank you very much!