Taxonomy data not found

[btredcup]

Hi,

Thanks for great tool. I am having an issue with taxonkit, I have downgraded it to v.0.11.1.

This is the error I am receiving after running taxonkit create-taxdump:

[ERRO] taxonomy data not found, please download and uncompress ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz, and copy "names.dmp", "nodes.dmp", "delnodes.dmp", and "merged.dmp" to /home/users/.taxonkit

Any help would be greatly appreciated. Thanks

[apcamargo]

taxonkit needs you to have a taxdump in your home. Just download it from the link in this error message and copy the files to ~/.taxonkit.

[btredcup]

That worked, thank you. Is that the same as the next step in the tutorial?

# Download the NCBI taxdump
aria2c -x 4 "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
mkdir ncbi-taxdump
tar zxfv taxdump.tar.gz -C ncbi-taxdump
rm taxdump.tar.gz

Or do I need to download it again and put it in ncbi-taxdump?

[apcamargo]

I think you can skip it, as long as you point to the right directory in this command:

awk '{print $2}' prot.accession2taxid.FULL \
    | sort -u \
    | taxonkit --data-dir ncbi-taxdump lineage \
    | rg "\tViruses;" \
    | awk '{print $1}' \
    > virus_taxid.list

[btredcup]

Thank you. Do I direct it to the ./taxonkit directory I downloaded the taxdump.tar.gz into initially? Or ictv-taxdump directory generated after running fix_taxdump.py?

From: Antônio Camargo @.> Sent: 10 August 2022 17:48 To: apcamargo/ictv-mmseqs2-protein-database @.> Cc: Newberry, Fiona @.>; Author @.> Subject: Re: [apcamargo/ictv-mmseqs2-protein-database] Taxonomy data not found (Issue #3)

I think you can skip it, as long as you point to the right directory in this command:

awk '{print $2}' prot.accession2taxid.FULL \

| sort -u \

| taxonkit --data-dir ncbi-taxdump lineage \

| rg "\tViruses;" \

| awk '{print $1}' \

> virus_taxid.list

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[apcamargo]

ncbi-taxdump is the one you download from NCBI. The one you generate is the ictv-taxdump

[btredcup]

Okay, thank you. All sorted now