Question: This job was terminated because it used more memory than it was allocated (new post)
gravatar for BC357
3.8 years ago by
United States
BC35770 wrote:

To Galaxy,

I've read on this forum about the proposed solutions to this memory issue. Other than applying for AWS grant, it's not clear if there is any "short-term" solution.

My current situation is

  • I run analyses on
  • most prior runs were fine in terms of the "memory" allocation.
  • last run (6.4 GB pileup data running with Varscan) has repeatedly been terminated due to the memory issue (like what another user has mentioned, some successful runs (with identical parameters) in the past were also of the same size)
  • I tried "re-run" a couple of times - actually a submission of a new request for Varscan run on the same pileup data. No success so far. I did wait for more than one hour between each submission

From what I read, please correct me for any misunderstanding, AWS grant is processed 4 times a year. Thus it seems that any technical run-in with memory on a random occasion would not be solved by AWS grant.

Q1. is 6.4 GB considered a big memory burden?

Q2. Any short-term/quick solution  to this current job?

Any suggestion? Thank you


processing memory • 1.0k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by BC35770
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Moving to a cloud (with or without an AWS grant) is most likely the solution. Setting up a local Galaxy is also possible, but requires more configuration and compute resources on your part.

The alternative is to try altering the parameters to be less compute intensive. Review the Varscan manual to determine how to do this and if the changes meet your research goals.

I will also review the memory allocated to this tool with our administrator.

Best, Jen, Galaxy

For reference:

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k
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