We have been having also been having this issue, we get empty TopHat output files. This is happening on two instances that were started within the past three weeks on the cloud. Cheers, Mo Heydarian ---------- Forwarded message ---------- From: 吳正華 <johnwu@ibms.sinica.edu.tw> Date: Fri, Oct 12, 2012 at 11:12 PM Subject: [galaxy-dev] Empty TopHat output To: galaxy-dev@lists.bx.psu.edu Hi all:**** ** ** After updating our local galaxy installation to the latest build last week, I found that when tophat finished its execution, all its output files showed empty in the history.**** ** ** However, I could execute the exact same command via shell and got correct tophat output files. **** ** ** It seemed that something went wrong when galaxy tried to copy tophat output files to galaxy databases/file.**** ** ** Did anyone encounter the same problem? How could I fix this problem?**** ** ** Thanks a lot.**** ** ** ** ** Best **** ** ** John Wu**** -------------------------------------------------------------**** PhD Student**** Academia Sinica**** ** ** ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/