AWS does have a lot of excellent documentation for doing just about everything, including an entire section for connecting to Windows server workspaces (https://docs.aws.amazon.com/AWSEC2/latest/WindowsGuide/connecting_to_windows_instance.html#rdp-prereqs). It took about 20 min following their guide to launch an instance, connect to it, map my drive to it, upload mothur and launch. It actually (embarrassingly) took me much longer to figure out PUTTY to transfer my files to the Linux server.
That being said, Windows does not have anything equivalent to the “screen” function in Linux so I would have to be connected the whole time. Also, being Windows, it’s much more circuitous to connect and transfer files than Linux (once I figured it out). Your advice is quite sound, but it’s being given to a pig-headed wannabe microbial ecologist who took it as a personal challenge to figure out how to run this on a Windows server In retrospect, I should have done all my analyses on the mothur image from the beginning. I’ll remember that for next time!
Thanks for the help, and the excellent blog on the subject. Without that, I would have been too intimidated to even try using AWS!