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

Cannot unlock directory #80

Closed
gevro opened this issue Jul 2, 2020 · 2 comments
Closed

Cannot unlock directory #80

gevro opened this issue Jul 2, 2020 · 2 comments

Comments

@gevro
Copy link

gevro commented Jul 2, 2020

Hi, Snakemake will not let me unlock the directory.
I am running snakemake --unlock, but I'm still getting this when I run the drop pipeline:

check for missing R packages
Structuring dependencies...
Dependencies file generated.

Building DAG of jobs...
Unlocking working directory.
check for missing R packages
Structuring dependencies...
Dependencies file generated.

Building DAG of jobs...
Executing subworkflow AE.
Structuring dependencies...
Dependencies file generated.

Building DAG of jobs...
Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:
/gpfs/scratch/evrong01/droptest/.drop/modules/aberrant-expression-pipeline
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.

@gevro
Copy link
Author

gevro commented Jul 2, 2020

Is there any way to run DROP without snakemake?
Snakemake causes many problems and bugs, and is generally not a good system.

Update: If I run drop update it fixes the problem. It is still a bug though. snakemake --unlock should work.

@vyepez88
Copy link
Collaborator

vyepez88 commented Jul 2, 2020

Execute snakemake unlock, without the --.
DROP is fully based on snakemake.

@gevro gevro closed this as completed Jul 11, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants