The Stampede cluster experienced some issues this last week. Please see this post from our administrator Nate about the options. C: Problems with TopHat
Your job may or may not go through as-is, but follow his advice concerning the size of the job and which cluster to use (default could be a better choice).
Best, Jen, Galaxy team
Thankyou for your reply . I have been running tophat using default and as per the suggestion i have also used Stampede . The job on default source is running since 5 days and on Stampede it was running fine , my datasets were yellow yesterday but today again they are grey which indicates that it is waiting for run. Is that possible? Regarding memory quota i have checked my account and there is enough memory for this job.