Troubleshooting

Frequently Possibly Asked Questions

I get an error about snakemake cannot lock directory when I try to call scprocess run

To avoid nasty surprises, scprocess locks several directories before running. If you cancel a scprocess run (or it otherwise gets stopped unexpectedly), this locking can remain. To fix this, you can run scprocess run config-my_project.yaml --unlock. This should give you a message about snakemake unlocked the directory, and then you run scprocess run config-my_project.yaml as normal.

One of my rules times out/fails after reaching memory limit

When a Snakemake rule fails, the error message typically specifies the exact rule name, for example: Error in rule run_mapping. To resolve resource-related errors you can override the default resource limits in your configuration file. For instance, to allocate 16 GB of memory and 60 minutes of runtime to the run_mapping rule, add the following to your config:

resources:
  gb_run_mapping: 16 # memory in GB
  mins_run_mapping: 60 # runtime in minutes

For more information please see the Reference section.

Bug reporting

If you encounter any problems when running scprocess please consider opening an issue on our GitHub.