Potential Errors - JoshLoecker/MAPT GitHub Wiki

This is a series of possible errors that may occur when trying to execute the pipeline
Note: Not all errors are listed here. If you find errors while running the pipeline, please submit an Issue

Command Line Errors

-bash: snakemake: command not found

Reason: You have not activated the conda environment. Bash does not know what to do with the command snakemake.
Solution: Activate the conda environment, found at /project/brookings_minion/conda-envs/mapt_pipeline. This can be done by executing conda activate /project/brookings_minion/conda-envs/mapt_pipeline

Snakemake Errors

[guppy/error] main: GPU mode not available in this build.

Reason: A GPU is not available. This arise from multiple scenarios

1. Not requesting a gpu node. Ensure you have done this in your srun or SLURM commands
2. Not passing the --singularity-args="--nv" in your snakemake command
   a. This should be done whenever calling snakemake -j all --use-singularity --singularity-args="--nv", assuming you need Guppy Basecalling

Solution: Always include the flags --use-singularity --singularity-args="--nv" whenever you have a GPU node

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