"snakemake --cores 1 --profile ../south-usa-sarscov2/profiles/south-central/" does not work

#1

Hi, I’m new to nextstrain, and get confused about this snakemake command, following this link: Setup and installation | Tutorial: Using Nextstrain for SARS-CoV-2
When I run this snakemake command, I get the following

(nextstrain) MacBook-Pro:ncov (nextstrain) MacBook-Pro:ncov snakemake --cores 1 --profile …/south-usa-sarscov2/profiles/south-central/
Error: profile given but no config.yaml found. Profile has to be given as either absolute path, relative path or name of a directory available in either /Library/Application Support/snakemake or /Users/nana/Library/Application Support/snakemake.

It seems like the file south-usa-sarscov2 is also not found anywhere. Any comments are greatly appreciated.

#2

Hi @emtf, welcome!

It looks like you’re trying to use @emmahodcroft’s southern USA build?

Unless the copy/paste of the error message went wrong, I suspect the issue is that the path:

should only have two leading periods/dots (../) instead of three.

Let us know if that solves your problem!

#3

Hi, @trs, thank you for your reply. I think I have used two leading periods/dots, not three.

#4

Ok. Do you have @emmahodcroft’s southern USA build cloned as a sibling directory of the ncov clone then?

#5

oh. I see. I will have that build cloned as a sibling directory.