Question: RNA Star: Problem with tool
gravatar for wcheng
12 months ago by
wcheng10 wrote:


I've been trying to transition from Tophat to RNA Star for my aligner. With just default parameters I received this error; "Tool Error : Remote job server indicated a problem running or monitoring this job". I have seen some posts about cluster issues and was wondering if this is maybe a bug or due to my input.

Thank you

ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson25k • written 12 months ago by wcheng10
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson25k wrote:


RNA STAR is not known to be associated with the current metadata issues at with certain mapping tools (details here).

Even if the same data used with work with Tophat, it is still a good idea to start by checking your inputs when this type of error results. You might also want to try using HISAT2 instead, as RNA STAR uses more resources and can fail for memory reasons with certain inputs (some resource failures will report with the error you describe).

Please see:

If you cannot find the problem, and are working at or can reproduce the error there, a bug report can be sent in. Please leave all inputs/outputs undeleted and include a link to this post in the comments. If there is a true issue with the tool itself, we definitely want to clarify the root problem and get it fixed. No examples of this specific error, for this tool, exist right now.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour