Hey, so Ive been trying to run a cuffquant job for about 72 hr. Its still in the queue and nothing has happen. There is no error, its just the job hasn't been done, but thats abnormally long time to wait. Its kind of time sensitive, but I really don't know how to fix this or expedite the process. Any suggestions. The other cuffquant job I ran was done in like an hour, and I submitted them seconds within each other, I don't understand why one would take such a long time.
Clusters have queues for different types of jobs. Most will have a wait time of 24 hrs at the longest (under ideal conditions). The server was busy over the week, increasing wait time a bit.
How jobs process: when one job completes, other jobs started up in your account will execute in the order submitted. This is per target cluster.
I reviewed the history associated with this long-queued job. It was deleted before the run started (it was still in queue - colored grey). Next time allow the job complete to keep your place in the queue by not deleting or deleting/rerunning.
More info if interested: https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute
Thanks, Jen, Galaxy team