error libmamba Non-conda folder exists at prefix

[Sofie8]

Hi Silas,

I have the 24.9.2 installation of miniforge: https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge-pypy3-24.9.2-0-Linux-x86_64.sh, but installation of atlas fails via mamba...

mamba create -y -n atlasenv metagenome-atlas=2.19.0

error:
slurm-57442481.zip

[bioinfogini]

Hi @Sofie8,
to me it solved by removing the "=2.19.0"
It is true that then it installed the 2.9.1 version, but no other way worked. Also, I suggest you first create the conda/mamba env and then install atlas

EDIT: also had similar issues in #739 , solved differently in that case

[Sofie8]

Hi @bioinfogini,

Thank you for your reply. I found it's the same as #1204.

When I have conda and mamba in /usr/bin/bash, snakemake throws this error:

[Atlas] �[32;21mINFO: Atlas version: 2.19.0�[0m
Config file /vsc-hard-mounts/leuven-data/314/vsc31426/miniforge/envs/atlas1/lib/python3.10/site-packages/atlas/workflow/../config/default_config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
/bin/bash: conda: command not found

When installing miniforge, you need to indicate 'no':

Do you wish to update your shell profile to automatically initialize conda?
This will activate conda on startup and change the command prompt when activated.
If you'd prefer that conda's base environment not be activated on startup,
   run the following command when conda is activated:

conda config --set auto_activate_base false

You can undo this by running `conda init --reverse $SHELL`? [yes|no]
[no] >>> no

Then either in atlas v 2.9.1 or v2.19.0 I get the libmamba error:

[Atlas] �[32;21mINFO: Atlas version: 2.9.1�[0m
Building DAG of jobs...
Creating conda environment /vsc-hard-mounts/leuven-data/314/vsc31426/miniforge/envs/atlas2/lib/python3.8/site-packages/atlas/workflow/rules/../envs/maxbin.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /vsc-hard-mounts/leuven-data/314/vsc31426/miniforge/envs/atlas2/lib/python3.8/site-packages/atlas/workflow/rules/../envs/maxbin.yaml:
Command:
mamba env create --quiet --file "/lustre1/project/stg_00091/atlas/conda_envs/47093a08f43ce325801fbadf31e2719a.yaml" --prefix "/lustre1/project/stg_00091/atlas/conda_envs/47093a08f43ce325801fbadf31e2719a"
Output:
error    libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

[Atlas] �[31;21mCRITICAL: Command 'snakemake --snakefile /vsc-hard-mounts/leuven-data/314/vsc31426/miniforge/envs/atlas2/lib/python3.8/site-packages/atlas/workflow/Snakefile --directory /lustre1/scratch/314/vsc31426/atlas/test_reads --jobs 30 --rerun-incomplete --configfile '/lustre1/scratch/314/vsc31426/atlas/test_reads/config.yaml' --nolock   --use-conda --conda-prefix /lustre1/project/stg_00091/atlas/conda_envs    --resources mem=179 mem_mb=183402 java_mem=152   --scheduler greedy  all  --resources mem=140 ' returned non-zero exit status 1.�[0m

I found the solution to this error here
downgrading mamba v2.0 to 1.
So installing atlas with: mamba create -y -n atlas1 metagenome-atlas=2.19.0 -c bioconda -c conda-forge
installs mamba v2 by default. I for now manually removed mamba in the atlas/env/bin and replaced it with a mamba version 1.5.9, now the error is gone (for now).

Hope this helps.

[bioinfogini]

Hi @Sofie8 ! Found the same solution as well today! Glad it is working for you, by now working for me as well! Fingers crossed!

[SilasK]

Thank you @Sofie8

I got the same problem, with libmamba. I installed the libmamba=1 inside the atlas env

I hope to find a better fix in the future