Question: HTseq runs fail
gravatar for gupta
14 months ago by
gupta20 wrote:


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 • 475 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson22k • written 14 months ago by gupta20

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 REPLYlink modified 14 months ago • written 14 months ago by gupta20
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson22k wrote:


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

That said, I made a request to have the memory allocation increased. Our team will respond with a decision on this ticket:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson22k
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