Question: Waiting to run for 6 days
gravatar for john.snowball
10 months ago by
john.snowball0 wrote:

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.

tophat jobs • 220 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson24k • written 10 months ago by john.snowball0

Hi John, We are looking at your account. More feedback soon. Jen, Galaxy team

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson24k
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hi John,

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:

  1. Wait another day to see if these start up. It could be that the queue they were scheduled against is busy.
  2. 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

ADD COMMENTlink written 10 months ago by Jennifer Hillman Jackson24k
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