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EichlerLab / smrtsv2

Structural variant caller
MIT License
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Killed job locked folder #18

Closed RSherman15 closed 5 years ago

RSherman15 commented 5 years ago

I killed a detect run which gave an error, but continued to hang, and now I get the following error:

Detecting variant signatures
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:
/work-zfs/mschatz1/rsherman/smrtSVRuns
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.

However, --unlock is not a recognized argument (either globally of smrtsv or of detect). I tried removing the whole detect folder, and still get the same error. How can I unlock the folder?

RSherman15 commented 5 years ago

As a temporary fix I added --unlock into line 137 of smrtsvrunner.py; that seemed to unlock the folder (and then did not actually run the detect command) so that I was then able to restart the run. Might be nice to add some way to do this from calling smrtsv, though.

paudano commented 5 years ago

You can also just remove .snakemake/locks/*. I might add an option or just document that.

bioabuliu commented 4 years ago

Just need to add --unlock after your command, then U can resart your run!