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

**URL:** <https://nextstrain.discourse.group/t/snakemake-cores-1-profile-south-usa-sarscov2-profiles-south-central-does-not-work/256>\
**Category:** Uncategorized\
**Created:** [January 5, 2021, 9:49am UTC](https://nextstrain.discourse.group/t/snakemake-cores-1-profile-south-usa-sarscov2-profiles-south-central-does-not-work/256 "2021-01-05T09:49:42Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![emtf](https://avatars.discourse-cdn.com/v4/letter/e/d9b06d/32.png) [@emtf](https://nextstrain.discourse.group/u/emtf)\
**Post date:** [January 5, 2021, 9:49am UTC](https://nextstrain.discourse.group/t/snakemake-cores-1-profile-south-usa-sarscov2-profiles-south-central-does-not-work/256/1 "2021-01-05T09:49:42Z")

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Hi, I’m new to nextstrain, and get confused about this snakemake command, following this link: [https://nextstrain.github.io/ncov/setup.html](https://nextstrain.github.io/ncov/setup.html)  
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.

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**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\
**Post date:** [January 5, 2021, 5:50pm UTC](https://nextstrain.discourse.group/t/snakemake-cores-1-profile-south-usa-sarscov2-profiles-south-central-does-not-work/256/2 "2021-01-05T17:50:34Z")

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Hi @emtf, welcome!

It looks like you’re trying to use @emmahodcroft’s [southern USA](https://github.com/emmahodcroft/south-usa-sarscov2) build?

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

> [@emtf](#):
>
> `.../south-usa-sarscov2/profiles/south-central/`

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

Let us know if that solves your problem!

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**Author:** ![emtf](https://avatars.discourse-cdn.com/v4/letter/e/d9b06d/32.png) [@emtf](https://nextstrain.discourse.group/u/emtf)\
**Post date:** [January 6, 2021, 12:56am UTC](https://nextstrain.discourse.group/t/snakemake-cores-1-profile-south-usa-sarscov2-profiles-south-central-does-not-work/256/3 "2021-01-06T00:56:44Z")

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

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<div class="post-metadata">

**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\
**Post date:** [January 6, 2021, 7:43pm UTC](https://nextstrain.discourse.group/t/snakemake-cores-1-profile-south-usa-sarscov2-profiles-south-central-does-not-work/256/4 "2021-01-06T19:43:40Z")

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Ok. Do you have @emmahodcroft’s [southern USA](https://github.com/emmahodcroft/south-usa-sarscov2) build cloned as a sibling directory of the `ncov` clone then?

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<div class="post-metadata">

**Author:** ![emtf](https://avatars.discourse-cdn.com/v4/letter/e/d9b06d/32.png) [@emtf](https://nextstrain.discourse.group/u/emtf)\
**Post date:** [January 8, 2021, 1:06am UTC](https://nextstrain.discourse.group/t/snakemake-cores-1-profile-south-usa-sarscov2-profiles-south-central-does-not-work/256/5 "2021-01-08T01:06:03Z")

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