Hello.
I've been trying to run TopHat analysis on a dataset for over a week, it keeps getting stuck on waiting to run, I've tried to rerun the dataset, re-upload it just to be sure, and the other tools seem fine but the TopHat steps seems to struggle.
Regards Fredrik
Hello,
My guess is that you are not allowing the jobs to stay in the queue long enough to move to the execution stage. Deleting gray jobs and restarting them almost always results in additional delays, because the original job's placement in the queue is lost, and the new job (like all new jobs) enters the queue at the end.
Try leaving the jobs queued. If they are gray for longer than a day or so, write back and we can take a closer look on Monday. Please make sure the history and gray jobs are not deleted if you decide to ask for review/feedback.
Related help topics that explain how jobs process in more detail are in this area of the Galaxy Hub https://galaxyproject.org/support/#datasets-and-histories. Specifically, see:
Cheers! Jen, Galaxy team
