Closed melodymale closed 1 year ago
Hey, I am getting the same error! Did you figure out how to solve this? Thanks
Hi @MelodyMale and @PeymanDerik , Thanks for your patience. The checkm2 environment recipe might not be robust or there may be an issue with your conda settings.
Let's start by listening to the warning in the conda code:
Your conda installation is not configured to use strict channel priorities.
This is however crucial for having robust and correct environments (for details,
see https://conda-forge.org/docs/user/tipsandtricks.html). Please
consider to configure strict priorities by executing
'conda config --set channel_priority strict'.
The bioconda, conda-forge, and defaults channels should really be prioritized in that order. Try this and see if it fixes the issue.
Alternatively, you can try a lightweight version of the environment to see if that helps.
Copy/paste this into your checkm2.yml
and try again:
name: checkm2_env
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- checkm2=1.0.1
It may cause the same initial issue, but could be another workaround.
Let me know if you have success with either option.
@dportik Thank you for your solution, it worked!
Noting that this is now addressed in #54
I'm trying to run this command
snakemake --snakefile Snakefile-hifimags.smk --configfile configs/Sample-Config.yaml -c8 --use-conda
But got a problem with create env via checkm2.yml
Here is my log