I recently encountered a problem when trying to run Cufflinks on eight BAM
files on our galaxy instance (via the multi-input toggle) and received the
error: "Unable to run job due to a misconfiguration of the Galaxy job
running system" for some, but not all, of the cufflinks jobs that appear in
the history. These particular BAM files were copied over from the history of
a larger workflow where they were successfully run through cufflinks. In the
case of the problem workflow run, the cufflinks jobs are all successfully
submitted to Torque PBS and continue to run and finish but many have this
error displayed in the History. The jobs with the error displayed fail to
copy files from the working directory to the database directory despite
running to completion. We recently updated to galaxy-central changeset
6131:be6c89c33639. I have seen this error multiple times for this workflow,
even after restarting galaxy. Does anyone have any ideas of what might be
going wrong?

Thanks for any help,
Andrew Warren
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