Question: How to resolve the reason for job was terminated
gravatar for wyyphysiology
15 months ago by
wyyphysiology0 wrote:

Hello, Recently, I have some RNA-seq data to analysis using Galaxy. Now I have a question and problem: during the Cuffdiff process, always have a note " This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help." but my account size was used 6% in memory. I do not know how to solve this question. Please help me. Thank you.

rna-seq • 579 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by wyyphysiology0

This message is relevant to the RAM of the machine that ran the job, not your quota. How large are you inputs?

ADD REPLYlink written 15 months ago by Martin Čech ♦♦ 4.9k
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


How to troubleshoot this type of error is covered here:

In short, try this (all are covered in the link above with more detail):

  • Check the inputs (content, format, metadata)
  • Verify the tool settings (example: check for database/genome mismatches)
  • Try a test re-run on a sub-sample of the data to determine if the full data size being "too large" is really a factor. For example, with Cuffdiff, try restricting the analysis to a single chromosome (filter the input BAMs down to a single chrom, then use those as test input).
  • If all checks out, then the job really is too large to run on the target server/cluster. Moving to your own Galaxy is a common solution when working with very large data.

If you cannot determine if there is an input or settings problem, would like direct feedback, and are working at and/or can reproduce the problem there, a bug report can be sent in.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
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