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Question: error code 139 while running cuffdiff on galaxy
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gravatar for kudzu
6 months ago by
kudzu • 10
United States
kudzu • 10 wrote:

Though my data set doesnt have replication, it should run right? but running the cuffdiff shows follwoing error: what can i do for this? Thank you error An error occurred with this dataset: Fatal error: Exit code 139 () [17:25:49] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [17:26:14] Inspecting maps and determining fragment length distributions. [17:34:12] Modeling fragment co
error rna-seq galaxy input cuffdiff • 206 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by kudzu • 10
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

This can indicate a server-side problem or more commonly an input problem.

First, double check your inputs. This is how: https://galaxyproject.org/support/#troubleshooting

If you cannot find the problem, and are working at Galaxy Main https://usegalaxy.org or can reproduce the problem there, a bug report can be sent in (green bug icon inside the red error dataset). Leave all inputs and outputs undeleted, including any tests you did to confirm proper input content/format. Please also include a link to this Biostars post in the comments.

The alternative is to skip over trying to troubleshoot this problem entirely and instead use the newer RNA-seq methods described in the Galaxy tutorials. Cuffdiff is an older tool and is not really recommended anymore. https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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