problem with mamba
Closed this issue · 6 comments
Hello,
I have found the same mistakes, but none of the suggested solutions helped,
Please have anyone can help with this issue?
I have installed mamba - mamba 1.5.11
But It didn't changed anything
"""
[Atlas] ^[[32;21mINFO: Atlas version: 0+unknown^[[0m
Config file /fs/s_alla/s_alla/atlas/atlas/workflow/../config/default_config.yaml is extended by ad$
Building DAG of jobs...
Creating conda environment ../atlas/atlas/workflow/envs/spades.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /fs/s_alla/s_alla/atlas/atlas/workflow/rules/../envs/spade$
Command:
mamba env create --quiet --file "/fs/s_alla/s_alla/el/databases/conda_envs/9eaf9b2b1db3541ec65$
Output:
error libmamba Non-conda folder exists at prefix
critical libmamba Aborting.
[Atlas] ^[[31;21mCRITICAL: Command 'snakemake --snakefile /fs/s_alla/s_alla/atlas/atlas/workflow/S$
""""
My slurm script looks this way -
""""
#!/bin/bash
#SBATCH --job-name=atlas
#SBATCH --nodes=2
#SBATCH --ntasks=50
#SBATCH --mem=125000M
source /home/s_alla/fs/s_alla/anaconda3/etc/profile.d/conda.sh
conda activate atlas-dev
atlas run all --working-dir /home/s_alla/fs/s_alla/el/ --jobs 10
conda deactivate
"""
Thank you,
Best,
Alla
I guess this is related to #742
What snakemake version do you have? use snakemake --version
Yes, it's the same issue.
Oops, it said I didn't have snakemake:)
Let me install it and try.
Thank you,
Best,
Alla
Still the same issue
snakemake --version
8.25.5
Config file /fs/sh_alla/sh_alla/atlas/atlas/workflow/../config/default_config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Creating conda environment ../atlas/atlas/workflow/envs/species_clustering.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /fs/sh_alla/sh_alla/atlas/atlas/workflow/rules/../envs/species_clustering.yaml:
Command:
mamba env create --quiet --file "/fs/sh_alla/sh_alla/el/databases/conda_envs/445be2af488f9a2a8f179c34e6b19311_.yaml" --prefix "/fs/sh_alla/sh_alla/elbrus/databases/conda_envs$
Output:
error libmamba Non-conda folder exists at prefix
critical libmamba Aborting.
[Atlas] ^[[31;21mCRITICAL: Command 'snakemake --snakefile /fs/sh_alla/sh_alla/atlas/atlas/workflow/Snakefile --directory /fs/sh_alla/sh_alla/el --rerun-triggers mtime --jobs$
I limited atals to snakemake v 7. I heard the snakemake developpers toped using mamba.
So you might try to install snakemake-minimal >= 7.18.1, <7.26
you can also try to use conda. (with libmamba, it is as fast as mamba)
I got the same problem, with libmamba. I installed the libmamba=1.59 inside the atlas env
I hope to find a better fix in the future