Run!

First run takes longer as containers need to be built.

Load the conda environment like conda activate GAME_env and in the GAME folder run:

On HPC/Server/Cluster using Slurm:

nohup snakemake --profile execution/slurm &

On Local Computer:

nohup snakemake --profile execution/local &

About the Command:

• nohup runs Snakemake in a way that won't be interrupted if you lose connection to the server/cluster
• The trailing & runs the command in the background, allowing you to continue using the terminal

Dry Run (Recommended):

Before running the full pipeline, perform a dry run to check what will execute and catch any errors:

snakemake --profile execution/slurm --dry-run

You can also inspect:

• GAME_results/data_config.yaml
• GAME_results/download_manifest.json

Common Troubleshooting:

• If your process was killed or stopped abruptly, Snakemake might complain about incomplete files when you try to run it again. We can tell Snakemake to identify and rerun those incomplete parts (and always a good idea to try a dry-run first):

snakemake --profile execution/local --rerun-incomplete —dry-run

• If Snakemake was suddenly killed, it might leave a hidden lock on your working directory to prevent other processes from overwriting files, and will tell you the directory is locked. You need to unlock it first before proceed with the run command: snakemake --unlock