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Question: HTseq runs fail
1
gravatar for gupta
2.5 years ago by
gupta • 30
gupta • 30 wrote:

Hi,

I am unable to execute HTseq on my data. I receive the following error message: 'This job was terminated because it used more memory than it was allocated.'

I am currently using only 55% of the space allotted to my account on the Galaxy main server. Do I need more space to run HTseq?

I would be grateful to receive your help. Best, PG
rna-seq galaxy • 923 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by gupta • 30

I read previous posts regarding this error, and tested the suggestions on my problem, i.e.

  • Re-runs - I performed re-runs.
  • Input/parameter adjustments - There are not many parameters associated with this software that can be modified to reduce the memory requirement.

RESULT --> It still fails.

All my previous runs using Tophat and Cufflinks (which may require more memory than HTseq) always worked. It would be great if the 'allocated memory space' for HTseq on the galaxy server can also be increased, as HTseq is an integral part of the RNAseq pipeline.

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by gupta • 30
2
gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The memory requirements to execute the tool are unrelated to the memory associated with your account quota.

Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at http://usegalaxy.org: https://wiki.galaxyproject.org/Support

That said, I made a request to have the memory allocation increased. Our team will respond with a decision on this ticket: https://github.com/galaxyproject/galaxy/issues/2501

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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