#metadenovo, hello. I am having continuing problems with this pipeline. I am not sure that I understand what the issue is, but I wanted to ask a question about the pipeline script. I had to download the eukulele phylodb database and I used the following command to create the files needed > create_protein_table.py --infile_peptide reference.pep.fa \ --infile_taxonomy taxonomy-table.txt --outfile_json prot-map.json \ --output tax-table.txt --delim "/" --col_source_id Source_ID \ --taxonomy_col_id taxonomy --column SOURCE_ID The files are in a folder called "phylodb". In the nexflow metadenovo pipeline should I use --eukulele_dbpath ./phylodb \ or should the folder phylodb be moved in the eukulele folder? and should I use --eukulele_db phylodb \ or anything else? Any help will be greatly appreciated.

The argument to

--eukulele_dbpath

should be the directory in which your eukulele databases are, i.e. not

phylodb

but its parent. It would probably be best if you move

phylodb

to a directory called

eukulele

and use the latter for

--eukulele_dbpath

. I'll make sure to update the docs to make this clearer. (In my experience, the pipeline download of phylodb works fine, but some of the other databases fails.)

Thank you. So should I type --eukulele_dbpath ./eukulele ? where in the eukulele folder, there is the phylodb folder or just the phylodb files?

You should have a directory structure like

./eukulele/phylodb

and pass

--eukulele_dbpath ./eukulele

to the pipeline. (Since this is the default for the param, you actually don't need to pass anything except

--eukulele_db phylodb

.)

Thank you