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Troubleshooting

  • Error about 'module load' when R scripts are being executed: Modify the configuration at snakemake > cluster_modules > R and set this to null.
  • Errors when running R scripts on a SLURM cluster: Ensure the configuration at snakemake > cluster_modules > R is set correctly. For example, set it to R/4.1.2-foss-2021b.
  • Unable to install R dependencies: Ensure your cluster/computer has internet access. If necessary, you can install the dependencies manually. Refer to the setup instructions for details on how to install R dependencies manually.

General Issues

  • There is no vambn_config.yml file in the repository: Copy the default_vambn_config.yml file and rename it to vambn_config.yml. Modify the configuration as needed.