Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Directory cannot be locked if previous snakemake run failed #12

Open
clody23 opened this issue Aug 7, 2021 · 1 comment
Open

Directory cannot be locked if previous snakemake run failed #12

clody23 opened this issue Aug 7, 2021 · 1 comment
Labels
bug Something isn't working

Comments

@clody23
Copy link
Member

clody23 commented Aug 7, 2021

I often get this error when the first run fails and have to rerun the analysis. This occurs when I run MToolBox as:

MToolBox-variant-calling -rpk -j 5 --cluster-config cluster.yaml --latency-wait 60 --cluster 'sbatch -p cluster7 -n {cluster.threads} -t {cluster.time} -o {cluster.stdout}'

This is the error:
Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:

If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument.

@clody23 clody23 added the bug Something isn't working label Aug 7, 2021
@clody23
Copy link
Member Author

clody23 commented Aug 7, 2021

The way I usually solve this is to do:

MToolBox-variant-calling -rpk -j 5 --unlock

and then rerun the command line above

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant