Hi! I have a problem with RepeatMasker that has been mentioned before here: Missing or disappearing output RepeatMasker but in my case the fix is already there in the ProcessRepats so I dont really understand why the output folder disappears after the analysis is finished. I ve tried with options and without, as well as with a big file and a small one, but while I can see the folder with the results when the analysis is running when it is done everything disappears and I get no error messages. I am using RepeatMasker locally with RMBlast as default (I got an error when installing RMBlast, same as here: Error Invoking Makeblastdb , didn't do the softlink since I have no permission but RMBlast seemed to work when I did rmblast -h).
Any ideas on what could be wrong are more than welcome, thank you! /Katerina