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mmseq2 with ncbi nr data base taxonamy issue #856
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Probably you've solved it by now, but still. Have you tried using |
Thanks for your reply, I tried to run mmseqs nrtotaxmapping after “mmseqs createtaxdb nrDB tmp --ncbi-tax-dump ./taxdump/ --tax-mapping-file ./prot.accession2taxid” using command "mmseqs nrtotaxmapping accession2taxid/prot.accession2taxid nrDB output.tsv". The output.tsv is as below, should I replace nrDB_mapping with this file? 0 1047168 |
I think so. I'm looking at the code the mmseqs devs linked in the previous issue and it seems that's what their script does. You'll basically create the
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Thanks a lot @AndrazMarinc! That looks correct! You still have to call the |
Thanks a lot @AndrazMarinc and @milot-mirdita . It worked. Also I found another solution, the file "prot.accession2taxid" download from NCBI needs modification. Only two columns (accession.version and taxid) are needed to run createtaxdb. |
Dear mmseq2 team
I am trying to create taxonomy database for ncbi nr data base. First I downloaded nr.fa, taxdump and prot.accession2taxid. Then I ran the below commands
mmseqs createdb nr.fa nrDB
mmseqs createtaxdb nrDB tmp --ncbi-tax-dump ./taxdump/ --tax-mapping-file ./prot.accession2taxid
After a few hours, the run completed without error. However, file nrDB_mapping is empty. Could you please advise where I did wrongly?
Thanks a lot
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