I submitted 6 fastq files to be aligned using Tophat 6 days ago. 5 were aligned within 24 hours. However, the last has been "waiting to run" since I submitted the job last Tuesday. Is there a reason why only 5 of the 6 jobs would run right away. I really cant move forward until I have the last bam file. Please advise on what I should do or if I should try to align using a different system. Never have had issues with Galaxy before but could try installing and running Tophat on my personal computer.
There are two stalled Tophat jobs (10 total datasets) in your account history. Why is not exactly clear.
Since these were queued last Wednesday, and other reports of delayed jobs have started up, there are two choices:
- Wait another day to see if these start up. It could be that the queue they were scheduled against is busy.
- Rerun the jobs, then go back and permanently delete/purge the original jobs (this clears them from the queue).
We almost never advise to do the second choice, but for this specific case, at this specific time, it might be the quickest way forward for you. If you decide to start with the first choice, and the jobs do not start up within a day, then use the second choice. If for some reason any reruns also remain queued (grey) for longer than a day, please let us know.
Our apologies for the inconvenience! Jen, Galaxy team