Welcome @kerstin.muner
Hopefully we can help!
Would you like to share back your failure example? It is hard to guess what may be going wrong, even for memory failures, since these can be due to some small issue with the file formats too, and especially with this tool since the data inputs are so specific.
Or, if you want to try to troubleshoot yourself more first, try comparing your protocol’s input data to the example in this tutorial. Loading the inputs and running the tutorial’s workflow is one quick way to generate the full example for comparison.
You could also review at some prior Q&A involving the tool here for ideas about what to check. Most are tagged with rbc_mirdeep2 rbc_mirdeep2_mapper rbc_mirdeep2_quantifier . Most of these involved the format of one of the files and cover how those were resolved. The logs are usually informative and provide some clues!
Let’s start there! We’d like to help you to resolve this! 