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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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Unrecognized tax ID, tax name or tax_scope mode: 'auto' #467

Open Rhia15 opened 1 year ago

Rhia15 commented 1 year ago

Hi,

I have tried to run eggNOG v2.1.11 on a test dataset with both the conda environment and the github version but both of them have given me the same error "Unrecognized tax ID, tax name or tax_scope mode: 'auto'" I have used the command line python emapper.py -i test.fa -o test with python version 3.11.4.

I have looked at the previous issue which was raised based on the same error message and tried to create a brand new environment as recommended but this did not seem to work. I have tried this on two protein sequence datasets:

102566271 MAGSNLTDMTPSIFILNGIPGLEEAHLWISIPFCSVYLIAMVGNCGLLYLIWIEEALHRPMYYFLCMLTLTDIALSTSMMPKAMCIFWFKLKEVAFNTCLTQMFFIYTFSAMESGVVTLMALDRYVAICYPLRYATILTNTVIITAGAVTFLMSATVIMPLVLLARRLPFCHTNVVPHTYCNHMSVLKLACASIKTDTVYGLVLTLVIGGLDILCIFISYIMILRAVVSLSSKEARSKAFSTCTAHICTIITTYTPALIVILTPRIGGHSIAPHIQVLMANVYLLLPAILNPIIYGLKTKQIRESFLKIFIRGKASSDFGTRFTGTGKKC 128652741 MNTINMSSCHCQPEYFLLMGIPGLENHHFLLSIPFCAMYLLALVGNNLLIFIIATNESLHQPMYFFLTILAVTDLFLCSTTVPKTLTIFWFGSHEISFNDCLTQVFWIHFIFAVESAILLIMACDRFFAICKPLTYSATFTPSFIRKLLIIALVRGICIITPFVFLLKRLPFHKSNIISHTYCEHMGVARLATANIRINVVYGLIIAFGSTGIDLILIAVSYVVIIRTVVRLPASEARYKAFNTCVSHICVILMFYLPAFFSFIAHRIGHKHIPPRVHIMLANLYVLVPPMMNPLIYGVKTKEIRQKIIMLFSLFSYIPLIYLKVPTISCLHSPL

and one file format which looks like this:

Alligatormississippiensis_>102566271_genename=LOC102566271_proteinID=XP_006258091.2_protein=[olfactory MAGSNLTDMTPSIFILNGIPGLEEAHLWISIPFCSVYLIAMVGNCGLLYLIWIEEALHRPMYYFLCMLTLTDIALSTSMMPKAMCIFWFKLKEVAFNTCLTQMFFIYTFSAMESGVVTLMALDRYVAICYPLRYATILTNTVIITAGAVTFLMSATVIMPLVLLARRLPFCHTNVVPHTYCNHMSVLKLACASIKTDTVYGLVLTLVIGGLDILCIFISYIMILRAVVSLSSKEARSKAFSTCTAHICTIITTYTPALIVILTPRIGGHSIAPHIQVLMANVYLLLPAILNPIIYGLKTKQIRESFLKIFIRGKASSDFGTRFTGTGKKC

I was wondering if there is a problem with my input or If i need to specify anything? Any help will be grately appreciated! Thank you!

Cantalapiedra commented 1 year ago

Hi @Rhia15 ,

First of all, the formats that you shared don't look like fasta files to me. You should provide fasta files as input.

However, the error you get seems to be independent on whether you sequences are right or wrong. What is your OS? How exactly did you install and set up eggNOG-mapper?

Best, Carlos