Below is the issue originally reported by @rmcd-mscb
I think I may have found a possible bug in prms6. I'm bringing it up because I think at some point in your testing you'll encounter it. It occurs when you have relative paths to files in the control file such as ./pipestem/daymet.nc.
I had to change the code where it reads the nc file as such. you can see my hacked change here rmcd-mscb@731ba56 and the commit before this one. Basically, I changed the code to look for the last ".". You probably have a more elegant way to do this. This is just an FYI.