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!