tophat2 job canceled by administrator

Question: tophat2 job canceled by administrator

4.1 years ago by

sbarcy • 0

United States

sbarcy • 0 wrote:

Hello

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

thanks

Serge

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 COMMENT • link •

modified 4.1 years ago by Nate Coraor ♦ 3.2k • written 4.1 years ago by sbarcy • 0

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

I am using usegalaxy.org

Any news about this?

ADD REPLY • link modified 4.1 years ago • written 4.1 years ago by rjcmrodrigues • 0

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

ADD REPLY • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k

4.1 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

Are you using usegalaxy.org ?

ADD COMMENT • link written 4.1 years ago by Martin Čech ♦♦ 4.9k

4.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k

4.1 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k 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.

--nate

ADD COMMENT • link written 4.1 years ago by Nate Coraor ♦ 3.2k

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