We seem to have sorted out the problem of TopHat failing to run but now we have a new problem. When TopHat runs with a large genome (but not with small genomes), it finishes the run fine and all the data is there but the web interface falls over about 8 hours into the run and when we try to access the web based interface we get a Proxy Error. When we restart it all looks fine. This is the sort of errors our HPC people find:

Exception happened during processing of request from ('XXX.XXX.XXX.XXX', 32960)
Traceback (most recent call last):
  File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/pa
ste/httpserver.py", line 1053, in process_request_in_thread
Unexpected exception in worker <function <lambda> at 0x201caed8>
Traceback (most recent call last):
  File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/pa
ste/httpserver.py", line 863, in worker_thread_callback
Unhandled exception in thread started by <bound method Thread.__bootstrap of <Th
read(worker 118, stopped 1127647552)>>
Traceback (most recent call last):