Question: RNA Star: Problem with tool
0
gravatar for wcheng
27 days ago by
wcheng10
wcheng10 wrote:

Hello,

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 26 days ago by Jennifer Hillman Jackson23k • written 27 days ago by wcheng10
0
gravatar for Jennifer Hillman Jackson
26 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

RNA STAR is not known to be associated with the current metadata issues at https://usegalaxy.org 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 https://usegalaxy.org 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 26 days ago • written 26 days ago by Jennifer Hillman Jackson23k
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