Question: tophat2 job canceled by administrator
gravatar for sbarcy
4.0 years ago by
United States
sbarcy0 wrote:


I am running Tophat2 analyses . Recently all my attempts failed . Jobs are systematically canceled by an administrator. I am within quotas allowed for files space. How can I get more info about why is the job canceled so I can try to do something about it . Reporting the error does not really help either



Error message :

"This job failed because it was cancelled by an administrator.
Please click the bug icon to report this problem if you need help."
software error • 1.1k views
ADD COMMENTlink modified 4.0 years ago by Nate Coraor3.2k • written 4.0 years ago by sbarcy0

I'm also having the same problem with different tools such as Count covarities and Table recalibration.

I am using

Any news about this?

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by rjcmrodrigues0

The top level reply applies to all job types at this time. Thanks, Jen, Galaxy team

ADD REPLYlink written 4.0 years ago by Jennifer Hillman Jackson25k
gravatar for Martin Čech
4.0 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

Are you using ?

ADD COMMENTlink written 4.0 years ago by Martin Čech ♦♦ 4.9k
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Yes, please try restarting the jobs. Delete, then permanently delete the prior runs. The jobs would eventually run as-is, but for right now, this is the working solution for the quickest execution. 

This advice applies for jobs starting during this specific time frame only. Please see Nate's comments in these posts for more details about the recent situation (the Galaxy Main system administrator):
galaxy runs SLOW
slurmstepd error job exceeded memory limit (8034000 > 7864320) being killed

Our apologies for the inconvenience, Jen, Galaxy team


ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
gravatar for Nate Coraor
4.0 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

Hi Serge,

This job (and many of your others) failed because the job ran out of memory. Sorry for the misleading message, this is coming up because our cluster resource manager (Slurm) sets this job exit state (cancelled) when it kills jobs that exceed their memory limits. We'll work on improving the message.

The memory limit for these jobs is 32 GB so it's a bit surprising to me that your job is exceeding it. In the near future I'll be working on getting some reliable data on how much memory tools are using. In the meantime you will probably need to adjust the parameters or input datasets to control the amount of memory usage. Others with more Tophat experience can chime in here to provide some recommendations.


ADD COMMENTlink written 4.0 years ago by Nate Coraor3.2k
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