On Wed, Dec 5, 2012 at 4:27 PM, Shaun Webb <swebb1@staffmail.ed.ac.uk> wrote:
Thanks for your reply Peter
The other tools work fine. I noticed that the makeblastdb process was still running on the server even after Galaxy said the job was complete, but still no files appeared in this directory. I have killed that process for now and will play around with it and see if I can figure it out. I'll let you kno if I find something.
Shaun
OK... this could be a Galaxy issue rather than a tool issue. A few more details might help. For example, we run our Galaxy on a server which (currently) contains the storage on that server (on a DAS), and this is exported to our cluster. I therefore run IO-heavy CPU-light jobs on the Galaxy server itself (e.g. makeblastdb) whereas all the BLAST search jobs are on the cluster. The point about this is heavy-IO over a network storage device introduces more points for failure. In this case perhaps there is a time lag before the Galaxy server can see the new files makeblastdb wrote? Is there anything that might help in the Galaxy paster.log file? Peter