snakemake errors running demo

[kylekimler]

Hi ProteinCartography team,

I'm on an M2 mac running into some issues trying the snakemake demo. I have the conda environment all set up and activated. When I run the snakemake command:

snakemake --snakefile Snakefile --configfile demo/config_actin.yml --use-conda --cores 6

I receive: CreateCondaEnvironmentException: Could not create conda environment from /Users/kylekimler/Projects/.../ProteinCartography/envs/run_blast.yml: Command: mamba env create --quiet --file "/Users/kylekimler/Projects/.../ProteinCartography/.snakemake/conda/b1b83db7a7ba8aea84a0e931f8dfe832_.yaml" --prefix "/Users/kylekimler/Projects/.../ProteinCartography/.snakemake/conda/b1b83db7a7ba8aea84a0e931f8dfe832_" Output: Could not solve for environment specs The following package could not be installed └─ blast 2.14.0** does not exist (perhaps a typo or a missing channel).

I've tried installing foldseek and blast separately and adding to $PATH but it did nothing to help. Any suggestions?

[mezarque]

Hey Kyle, thanks for reaching out! We've had similar issues caused by conflicts between different versions of conda or different channels that work on different processors (Apple vs. Intel silicon).

Could you share the text that prints when you run conda info from your command line interface (e.g. Terminal)?

[jshanahan1]

Hello, I have a similar issue with the demo not being able to install Foldseek. I am using a 2021 MacBook Pro 14in M1 Pro. Here is the output from running "conda info":

active environment : cartography_tidy active env location : /Users/jackshanahan/miniconda3/envs/cartography_tidy shell level : 2 user config file : /Users/jackshanahan/.condarc populated config files : conda version : 23.7.4 conda-build version : not installed python version : 3.11.4.final.0 virtual packages : archspec=1=arm64 osx=13.5=0 __unix=0=0 base environment : /Users/jackshanahan/miniconda3 (writable) conda av data dir : /Users/jackshanahan/miniconda3/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/osx-arm64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-arm64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/jackshanahan/miniconda3/pkgs /Users/jackshanahan/.conda/pkgs envs directories : /Users/jackshanahan/miniconda3/envs /Users/jackshanahan/.conda/envs platform : osx-arm64 user-agent : conda/23.7.4 requests/2.29.0 CPython/3.11.4 Darwin/22.6.0 OSX/13.5 UID:GID : 504:20 netrc file : None offline mode : False

[kylekimler]

Hi Dennis, thanks, here's mine as well

active environment : cartography_tidy active env location : /Users/kylekimler/miniconda3/envs/cartography_tidy shell level : 2 user config file : /Users/kylekimler/.condarc populated config files : conda version : 23.5.2 conda-build version : not installed python version : 3.11.4.final.0 virtual packages : archspec=1=arm64 osx=13.4=0 __unix=0=0 base environment : /Users/kylekimler/miniconda3 (writable) conda av data dir : /Users/kylekimler/miniconda3/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/osx-arm64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-arm64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/kylekimler/miniconda3/pkgs /Users/kylekimler/.conda/pkgs envs directories : /Users/kylekimler/miniconda3/envs /Users/kylekimler/.conda/envs platform : osx-arm64 user-agent : conda/23.5.2 requests/2.29.0 CPython/3.11.4 Darwin/22.5.0 OSX/13.4 UID:GID : 501:20 netrc file : None offline mode : False

[mezarque]

Thanks for sending over this info!

Based on other similar issues we've had, I think this issue is caused by installing the macOS Apple M1 64-bit version of conda. It should be resolved by instead installing the macOS Intel x86 64-bit version of conda (see this page). I think the error is thrown because bioconda (which contains blast) doesn't yet support osx-arm64 architecture.

Even if you are running an M1 machine, you should be able to run the Intel x86 64-bit version of conda thanks to Rosetta, which should already be installed on your machine. You may have to open your Terminal or other CLI app using Rosetta, as described in the link above.

Let me know if this solves the issue; we can update our README to include more precise instructions for installing conda.

[kylekimler]

This method works great! Thank you! And thanks for teaching me about Rosetta