Question: error code 139 while running cuffdiff on galaxy
gravatar for kudzu
6 months ago by
United States
kudzu10 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

ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by kudzu10
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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

First, double check your inputs. This is how:

If you cannot find the problem, and are working at Galaxy Main 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.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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