binchicken build error

[ccgallen]

Hi! I am trying to set up binchicken and am encountering some problems with the build. Any idea what is wrong?

binchicken build --conda-prefix /data/ccallen/miniforge3/envs/ --singlem-metapackage /data/databases/S4.3.0.GTDB_r220.metapackage_20240523.smpkg.zb --gtdbtk-db /data/databases/gtdbtk_r220_data --checkm2-db /data/databases/CheckM2_database/uniref100.KO.1.dmnd
12/09/2024 09:51:38 PM INFO: Bin Chicken v0.12.6
12/09/2024 09:51:38 PM INFO: Command: binchicken build --conda-prefix /data/ccallen/miniforge3/envs/ --singlem-metapackage /data/databases/S4.3.0.GTDB_r220.metapackage_20240523.smpkg.zb --gtdbtk-db /data/databases/gtdbtk_r220_data --checkm2-db /data/databases/CheckM2_database/uniref100.KO.1.dmnd
12/09/2024 09:51:41 PM INFO: Building SingleM, CoverM and Prodigal conda environments
12/09/2024 09:51:41 PM INFO: Loading sample info
12/09/2024 09:51:41 PM INFO: Loading genome info
12/09/2024 09:51:41 PM INFO: Config file written to: /data/ccallen/miniforge3/envs/binchicken/build/build_coassemble/config.yaml
12/09/2024 09:51:41 PM INFO: Executing: snakemake --snakefile /data/ccallen/miniforge3/envs/binchicken/lib/python3.10/site-packages/binchicken/workflow/coassemble.smk --configfile '/data/ccallen/miniforge3/envs/binchicken/build/build_coassemble/config.yaml' --directory /data/ccallen/miniforge3/envs/binchicken/build/build_coassemble --cores 1 --rerun-incomplete --keep-going --nolock --conda-create-envs-only  --local-cores 1 --retries 3 --use-conda --conda-frontend mamba --conda-prefix /data/ccallen/miniforge3/envs/
Building DAG of jobs...
Creating conda environment /data/ccallen/miniforge3/envs/binchicken/lib/python3.10/site-packages/binchicken/workflow/env/prodigal.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /data/ccallen/miniforge3/envs/binchicken/lib/python3.10/site-packages/binchicken/workflow/env/prodigal.yml:
Command:
mamba env create --quiet --file "/data/ccallen/miniforge3/envs/d4b4e9183a4bc562b281d21ff275bc0d_.yaml" --prefix "/data/ccallen/miniforge3/envs/d4b4e9183a4bc562b281d21ff275bc0d_"
Output:
error   libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

[AroneyS]

Looks like an error due to mamba2. How did you install bin chicken? Downgrading mamba to v1.4 should fix.

[ccgallen]

Hi!

Thanks for the quick response. I did the following to install binchicken:

mamba create -n binchicken bioconda::binchicken

[AroneyS]

Looks like the bioconda recipe didn't pin mamba to the correct version. Can you try running conda install mamba=1.4.9 within the binchicken env?

[ccgallen]

Thank you that seems to have fixed it for now. It is currently installing and downloading remote packages.