Snakemake cluster status script for qsub
Entering edit mode
13 months ago
blackadder ▴ 30

Hello everyone,

I am running a snakemake workflow in my university cluster and after a while I noticed that the pipeline failed to recognize job failure. That resulted in jobs hanging indefinitely and new jobs were not being submitted in the cluster. I did a bit of search and I found out that other people had similar issues here. The solution apparently is a status script that controls jobs and handles the flow.

Snakemake official site has an example of a cluster status script here but is for slurm clusters.

Does anyone has a script for SGE systems that uses qsub?

Thank you!

snakemake cluster • 411 views

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