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-directoryrule_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