First of all it looks like repeatexplorer is a fairly specific pipeline with its own galaxy server and user registration. On the website https://repeatexplorer-elixir.cerit-sc.cz/ I see the following text:
If you need help with RepeatExplorer or you want to report a problem and our wiki is not able to give you answers, please contact server administrator.
I think the server administrator can give you a better answer.
If you ask your question to the server administrator you may need to clarify what you mean with rDNA and if “not found” is an error or an output message. I dont know the tool but I would guess that you get more output then just “not found” (I can be wrong ofcourse).
Do you mean recombinant DNA? And are it just fastq or fasta files? In addition to that if you do mean recombinant DNA I would guess it is very possible to not find satelites because mostly satelites are non-coding and recombinant DNA (created in a lab) is only coding.
I hope for now my reply is helpfull and maybe someone with experience with this tool will also see your post.