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Question: Cufflinks output empty
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gravatar for gupta
17 months ago by
gupta • 30
gupta • 30 wrote:

Hi,

I am encountering a problem similar to that mentioned here: https://www.biostars.org/p/45848/

I am on the main Galaxy server. I have 6 samples, and Cufflinks worked fine for 4 samples. The other two samples return an 'empty output'. I am running Cufflinks without any input annotation file and using the exact same workflow for all samples.

In general, job execution is taking extremely long (> a day for a single submission).

Can someone please help me resolve this issue? Thanks in advance.

Best, PG
cufflinks galaxy main • 349 views
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modified 17 months ago by Jennifer Hillman Jackson ♦ 25k • written 17 months ago by gupta • 30
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gravatar for Jennifer Hillman Jackson
17 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The job may be failing due to the size exceeding the memory or other cluster resources available at http://usegalaxy.org. However, I would suggest one more rerun given the recent server issues.

Please see here for server updates and links to troubleshooting help for failed job troubleshooting and alternative ways to use Galaxy for very large jobs: https://biostar.usegalaxy.org/p/23801/#23846

Thank you for reporting the problem! Jen, Galaxy team
ADD COMMENT • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k
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