Question: Tophat couldn't work.
gravatar for parakhpalak
22 months ago by
parakhpalak10 wrote:

I have been working on Tophat and it couldn't run. Continuously i got "Tool execution failed". How can i resolve this?

tophat • 568 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by parakhpalak10

Cluster failures like this have been occurring at over the last few days. The solution, if working there, is to re-run. If the same job fails repeatedly, first double check the inputs and should that not reveal a cause a bug report can be sent in.

Include a link to this post in the comments and leave all inputs/outputs undeleted.

If there is more to share from our admin, our team will follow up. Jen, Galaxy team

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k

Update: Checked with admins - the cluster/server has no known persistent issues. It will be restarting in a few minutes (another update in prep for 17.01 release), so wait just a bit, rerun, then if the error comes up again please do submit a bug report so we can review what exactly is going on.

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I found your account at, so there is no need to send in a bug report. Some Tophat jobs are successful, some failed for cluster problems earlier in the week, but the most recent jobs are now failing for this reason:

This job was terminated because it ran longer than the maximum allowed job run time. Please click the bug icon to report this problem if you need help.

This error indicates that the job runs longer than the allocated wall-time on the Galaxy Main server using default cluster resources. You can try running on a targetted cluster with a longer processing time (tool form option: Job Resource Parameters). Try Stampede and/or Jetstream. Full details about this and other options (including moving to a local/cloud Galaxy, if needed) are here:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k
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