Describe the bug
Mamba not detected in snakemake when hybracter is run on the cluster via slurm. hybracterENV installed with miniforge3.
To Reproduce
- conda activate hybracterENV in the submission script, then hybracter long for pacbio reads (including --no_medaka --flyeModel --pacbio-hifi ).
- Error message:
CreateCondaEnvironmentException:
The 'mamba' command is not available in the shell /bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with conda activate base.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with conda install -n base -c conda-forge mamba. If you still prefer to use conda, you can enforce that by setting --conda-frontend conda.
ERROR: Snakemake failed
Additional context
Interestingly, mamba is detected prior to activating the hybracter environment (which mamba), but snakemake fails saying it cannot find mamba. Also tried --conda-frontend conda instead, but receive the following error:
Activating conda environment: ../../../miniforge3/envs/hybracterENV2/lib/python3.12/site-packages/hybracter/workflow/conda/07b2ed8e593a2afce4f34d72461f46bd_
/bin/bash: /usr/bin/activate: No such file or directory
/bin/bash: line 1: filtlong: command not found
Describe the bug
Mamba not detected in snakemake when hybracter is run on the cluster via slurm. hybracterENV installed with miniforge3.
To Reproduce
CreateCondaEnvironmentException:
The 'mamba' command is not available in the shell /bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with
conda activate base.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed withconda install -n base -c conda-forge mamba. If you still prefer to use conda, you can enforce that by setting--conda-frontend conda.ERROR: Snakemake failed
Additional context
Interestingly, mamba is detected prior to activating the hybracter environment (which mamba), but snakemake fails saying it cannot find mamba. Also tried --conda-frontend conda instead, but receive the following error:
Activating conda environment: ../../../miniforge3/envs/hybracterENV2/lib/python3.12/site-packages/hybracter/workflow/conda/07b2ed8e593a2afce4f34d72461f46bd_
/bin/bash: /usr/bin/activate: No such file or directory
/bin/bash: line 1: filtlong: command not found