Question: CummeRbund error Troubleshooting
gravatar for v.venugopalan
15 months ago by
v.venugopalan0 wrote:

Hi I was doing CummeRbund analysis on my RNAseq samples and it shows the following message for some of them 'An error occurred with this dataset: Fatal error: Exit code 1 ()' If I try to view it, I can see the image. How to troubleshoot this problem? Or can I continue using the data for further analyses Many thanks Viji

rna-seq • 388 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by v.venugopalan0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There can be many reasons for errors. First, check to see if your use-case is related to the current known issue with CummeRbund listed here:

If different:

Have you reviewed the full error message? Often the reason for a problem is reported. (click on the bug icon to review)

Also, have you double checked the inputs and CummeRbund tool settings to eliminate common issues? Troubleshooting FAQs are here:

If inputs are confirmed as correct and problems persist, investigating to see if there is a tool problem requiring a correction is the next step. Should there be a true tool bug, we'll want to characterize and fix it.

Two options if the problem is new (unrelated to the known tool issue in the first link above):

1 - If you are working at or if you can reproduce the novel problem there, and you cannot determine the problem, a bug report can be sent in. Leave inputs and outputs undeleted and please include a link to this post so we can associate the two.

2- Otherwise, you can post the full error message along with the tool version in use, the options set that are not defaults, and the Galaxy version/server used. From there we can try to troubleshoot using that information as a guide. But please double check the inputs first - formatting issues and genome mismatches are the root cause of most errors and sometimes difficult to determine without examining the actual input data and/or a shared history.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson25k
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