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5. Troubleshooting

Authors
Affiliations
Department of Biology, San Diego State University, San Diego, California, USA
Department of Biology, San Diego State University, San Diego, California, USA

5.1. Restarting SaVor

If the workflow is killed or interrupted, append the --rerun-incomplete flag to the snakemake command. This allows regeneration of output files for rules that were in progress during the interruption.

snakemake -p --cores all --workflow-profile workflow-profiles/default --rerun-incomplete

If you had to manually interrupt the workflow or it was unexpectedly killed, the following command must first be executed before restarting SaVor:

snakemake -np --cores all --unlock
SaVor
4. Executing SaVor
SaVor
Savor Tutorial