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):

Do you have any suggestions for what is happening?

Best Wishes,

Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol

Tel. +44 117 3312058
Fax. +44 117 3312091


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