FAQ

QuaC workflow failed due to Error: Directory cannot be locked

See snakemake docs here on why snakemake locks the working directory. Error: Directory cannot be locked might happen when the parent snakemake process gets killed unexpectedly before completion. It is recommended to investigate why it got killed before proceeding to the next step. If you want to remove the lock (ie. unlock it), add -e='--unlock' to your original run src/run_quac.py command. Once that has completed you can run the original command again and the pipeline will pick up from it's last state.

How to view log files?

  • If --cli_cluster_config was used, logs from the snakemake process are stored in the directory provided using --log_dir. Else, logs will be directed to stderr/stdout and not stored in a file.
  • If --snakemake_cluster_config was used, logs for the jobs triggered by snakemake workflow are stored in sub-directory rule_logs/ under the directory provided using --log_dir. Else, logs will be directed to stderr/stdout.

How to cite QuaC?

Please cite this article:

Gajapathy et al., (2023). QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data. Journal of Open Source Software, 8(90), 5313, https://doi.org/10.21105/joss.05313