bedgraph-to-bigwig error

Welcome, @Adrian1

The tool is comparing the term in your file to the reference genome. If you are working at UseGalaxy.org, then mm39 would be a custom reference genome. Check the format of that fasta, and the custom “database” you created for it. Is the key unique, and it is assigned to your input data?

Help → Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at