David, What is the full stack trace that you're seeing? The stack trace is the text below "Traceback" and identifies the exact location where the problem occurs.
Are you following these guidelines: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup for setting up large genomes in Galaxy? Also, it would be ideal if you could upload the problematic data--genome + reads--to our public instance (main.g2.bx.psu.edu) and see if you can reproduce the problem that you're seeing. Thanks, J. On Dec 9, 2011, at 12:20 PM, David Matthews wrote: > Hi, > > 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, > David. > > __________________________________ > 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 > Bristol. > BS8 1TD > U.K. > > Tel. +44 117 3312058 > Fax. +44 117 3312091 > > d.a.matth...@bristol.ac.uk > > > > > > > ___________________________________________________________ > 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/
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