Including Picard tool in galaxy
Picard, like most tools, prints logs to stderr.
It should be in the Galaxy history. Are you using a version of picard from the toolshed (if so, which one)? You might set cleanup_job to never in the config, which will prevent galaxy from cleaning the working directory. This will enable seeing what the job actually produced.


Most likely there's more in the log file that you're not showing is us and picard itself never ran to completion. In lieu of that information, what I wrote above is usually sufficient to debug things.