Tophat ends without error message

Question: Tophat ends without error message

3.6 years ago by

jling • 70

United States

jling • 70 wrote:

Hi Galaxy,

I've been trying to use Tophat for the past week but I keep encountering an issue where the run appears to begin (turns yellow) and runs for a few hours but then reverts back to gray and says waiting to run (no error message).

After maybe 8 tries one of my samples worked but the other one still has this issue. I've tried reuploading the fastqsanger files and retrying but it doesn't appear to help.

Could someone tell me what is going on with Tophat? Does each Tophat run need to enter the queue twice or something?

Thanks

software reset no error message tophat • 871 views

ADD COMMENT • link •

modified 3.6 years ago • written 3.6 years ago by jling • 70

3.6 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

Hi,

Your job has reached the time limit in our default queue and has been resubmitted to the Stampede supercomputer at TACC. The wait time on Stampede is variable, but is typically less than 1 day.

I'll be putting up a bit of documentation shortly on how long the time limit for each tool is and some tips on how to get your jobs to run as quickly as possible. In the short term, if you use the job resource selector at the bottom of the tool form to select Stampede for jobs that you know will run longer than the time limit, you can avoid the initial queued -> run -> queued step.

ADD COMMENT • link written 3.6 years ago by Nate Coraor ♦ 3.2k

Documentation is updated here: https://wiki.galaxyproject.org/Main

ADD REPLY • link written 3.6 years ago by Nate Coraor ♦ 3.2k

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

What server are you working on? The public Main Galaxy at http://usegalaxy.org or somewhere else?

If another public Galaxy server, contacting the administrators of that instance is best. If using a local or cloud, the issue could be a resource or configuration issue - if this is it - please send more details and we can try to help troubleshoot.

Best, Jen, Galaxy team

ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

3.6 years ago by

jling • 70

United States

jling • 70 wrote:

I'm using the public server, yes (http://usegalaxy.org)

I just upload my fastqsanger files via FTP and run Tophat. I'm very familiar with Galaxy and have done this many times in the past, but for some reason I've been having trouble this past week.

ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by jling • 70

3.6 years ago by

jling • 70

United States

jling • 70 wrote:

I see, I'll change the Job Resource next time. Thanks

ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by jling • 70

Please log in to add an answer.

Similar posts • Search »