Ok, I found the problem and was able to reproduce it.
The “Jetstream” cluster is the problem.
Near the bottom of the tool form is an option to select the cluster to run the job on. You were using the default, which means Galaxy decides where to send the job. It will never send a mapping job to Stampede (and expect mapping jobs to fail there anyway, for a different reason). Galaxy will send mapping jobs to Jetstream – and since that is problematic, there is a way to avoid it.
Set up your tool form like this:
You’ll see this option first:
In the pull-down menu switch to “Specify job resource parameters” and then select the “Galaxy Cluster (default)” option:
I will alert our admin about this. More feedback soon. Meanwhile, this will allow you to get your jobs to run successfully.
Thanks for taking the time to follow through and share your history, much appreciated!