20 months ago by
As a quick guess, the sort order of the reference annotation used could potentially be a factor. Sort the GTF dataset by chromosome and start coordinate and re-run to see if that makes a difference (use the tool "Sort").
If that does not work, would you like to submit the problematic run as a bug report? This will allow us to look over the data and provide the best feedback.
Should you be executing the job on a local/cloud, if some portion of it can be replicated on http://usegalaxy.org and submitted as a bug, that will be enough. It the problem cannot be replicated on Main, then that is also useful information to know about.
This question was a bit difficult to track because of the update submitted as a reply to the original post (indicating a solution) instead of as a comment. I'll adjust that now.
Thanks, Jen, Galaxy team