Rename_table doesn't work with uniref90

I face an error when trying to attach names to features
I used uniref90 to run humann.

humann2 --input kclsho.fq.gz --nucleotide-database /resources/chocophlan/ --protein-database resources/uniref90


humann2_rename_table --input kclsho_genefamilies.tsv --output kclsho_genefamilies-NAMES.tsv --names uniref90

And here is the error…

usage: humann2_rename_table [-h] [-i INPUT]
[-n {infogo1000,metacyc-rxn,kegg-module,ec,go,metacyc-pwy,pfam,eggnog,uniref50,kegg-pathway,kegg-orthology}]
[-c CUSTOM] [-s] [-o OUTPUT]
humann2_rename_table: error: argument -n/–names: invalid choice: ‘uniref90’ (choose from ‘infogo1000’, ‘metacyc-rxn’, ‘kegg-module’, ‘ec’, ‘go’, ‘metacyc-pwy’, ‘pfam’, ‘eggnog’, ‘uniref50’, ‘kegg-pathway’, ‘kegg-orthology’)

When I try using any of the suggested names it renames 0, as all features start from “'UniRef90_” which seems incompatible.

Any hints, please?

Hello, Sorry for the confusion. The uniref90 name mapping files are large so we can’t include them in the pypi/conda package. You can download them with the other large utility files with the following command:

$ humann_databases --download utility_mapping full $DIR (replace $DIR with the location to store the files)

Once these files are downloaded you will be able to select uniref90. Sorry again for any confusion.

Thank you,

Thank you very much for the swift reply, Lauren.
I will give it a go.