issues with sortmeNRA

usegalaxy.org support
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I am encountering issues with sortmeRNA. The jobs are terminated because it used more memory than it was allocated. I am not sure why. I’ve tried to remedy this issue by reducing the parameters (e.g., limiting the number of input databases, etc.).

sortmeRNA has only worked for me once before, but now each time I run it the job fails…any help is appreciated. Thanks!

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Welcome, @cjspiegel

If any job is failing for memory reasons, that usually indicates a problem with the inputs or the parameters, so start by checking those items first.

More details → error with Picard's MarkDuplicates - This job was terminated because it used more memory than it was allocated. - #2 by jennaj

So, in general, for troubleshooting this tool:

  • Run checks on the read content and format (FastQC, or Fastq info)
  • Then, make sure you are choosing form options that fit your data.
  • A test with a tiny dataset can sometimes help to learn where things are going wrong, too, but it sounds like you are already trying that…

There is another known issue with the tool that we are working on, details about that part here. This only impacts jobs at UseGalaxy.org, so the solution for this one is to run the job at UseGalaxy.eu or UseGalaxy.org.au instead for now. → SortMeRNA not working following the Metatranscriptomic Workflow Tutorial - #6 by jennaj

The error message from that known issue is a little bit different from what you describe, or maybe I am misunderstanding, or something changed. You are welcome to share back a link to your history and I’ll take a look. How to generate that is covered in the banner topic at this forum, or see here directly. → How to get faster help with your question

Let’s start there, thanks! :slight_smile: