Hi All, Thanks to this email from Peter Cock I was able to find what was causing the error I initially described here. I also now have a theory of why this is happening.
My unconfirmed guess. When a colon is present in the standard output or standard error file, someone betweent Galaxy, python-drmaa, pbs-drmaa, Torque or Maui recognize this as a scp syntax, like: user@host:/path/to/file And then choose to at 'galaxy@' in from of what is really a filesystem path. This is why I'm seeing this kind of error: Unable to copy file /var/spool/torque/spool/1013.head.OU to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.OU By using Peter's ".replace(":", "_")" trick on "lib/galaxy/jobs/runners/drmaa.py" I was able to make this issue go away. As Peter mention this is a very dirty fix and I'm sure there has to be a much cleaner way of fixing this issue. http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-instead-of-SGE-td4657848.html http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-torque-and-nfs-td4657294.html I'll be opening a ticket on Trello to follow the progress on this issue. Regards, Carlos ___________________________________________________________ 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/