These particular jobs were a success, but a small issue with cluster paths is still under correction. Once implemented, this fix will resolve the automatic metadata assignments going forward.
What to do now:
For the green success Tophat jobs with the metadata warning: Click on the link in the smaller yellow warning box ("Set it manually or retry auto-detection").
For the cluster failed Cufflinks job in your other history: Please rerun this job now. Jetstream is still having a few hiccups with jobs and rerunning is the solution. If the rerun fails again now, sending in a bug report from the new error dataset would be helpful for us to diagnose. https://wiki.galaxyproject.org/Support#Reporting_tool_errors
For any others reading that run into either of these problems, please do the same.
Thanks again for reporting the issue with Tophat. Much appreciated as it uncovered a true problem that we thought was fixed, but not in all cases.
Jen, Galaxy team