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Question: Using more memory than what allocated
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gravatar for VY
2.5 years ago by
VY • 120
London
VY • 120 wrote:

I keep getting this message when running cuffdiff "This job was terminated because it used more memory than it was allocated", I've read the wiki thread and the only way I can bypass this is if I set up my own instance of galaxy on the cloud.

Is there anyway to avoid that, or to increase the allocated memory?

Please help :(
memory quota • 817 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by VY • 120
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

This specific tool already executes with maximum memory allocation on the cluster at http:/usegalaxy.org.

Choosing options that reduce memory utilization are sometimes possible. The same memory-intensive options used line-command also apply when executed within Galaxy. The manual explains these in more comprehensive detail: http://cole-trapnell-lab.github.io/cufflinks/

However, those changes may not meet your analysis needs or the data may be too large to processes even with the changes. A local or cloud is the only solution for these cases (it is doubtful that other public Galaxy servers allocate more memory - but you could try for those that offer open accounts). https://wiki.galaxyproject.org/BigPicture/Choices

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