On Dec 12, 2011, at 5:25 AM, David Matthews wrote:

Hi,

Many thanks for the feedback. Sorry about missing some of the traceback, here is the full traceback:

Exception happened during processing of request from ('xxx.xxx.xxx.xxx', 32781)

Traceback (most recent call last):

File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread

  self.finish_request(request, client_address)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 322, in finish_request

  self.RequestHandlerClass(request, client_address, self)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 617, in __init__

  self.handle()

File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle

  BaseHTTPRequestHandler.handle(self)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/BaseHTTPServer.py", line 329, in handle

  self.handle_one_request()

File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 421, in handle_one_request

  self.raw_requestline = self.rfile.readline()

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/socket.py", line 444, in readline

Unexpected exception in worker <function <lambda> at 0x2aab12fa9f50>

Traceback (most recent call last):

File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 863, in worker_thread_callback

  runnable()

File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1037, in <lambda>

  lambda: self.process_request_in_thread(request, client_address))

File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1056, in process_request_in_thread

  self.handle_error(request, client_address)

File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1044, in handle_error

  return super(ThreadPoolMixIn, self).handle_error(request, client_address)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 338, in handle_error

  traceback.print_exc() # XXX But this goes to stderr!

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 233, in print_exc

  print_exception(etype, value, tb, limit, file)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 125, in print_exception

  print_tb(tb, limit, file)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 69, in print_tb

  line = linecache.getline(filename, lineno, f.f_globals)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 14, in getline

  lines = getlines(filename, module_globals)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 40, in getlines

  return updatecache(filename, module_globals)

File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 131, in updatecache

  lines = fp.readlines()

MemoryError

Hi David,

It looks like something is trying to read way too much data into something else, probably the response.

1. is debug = True?
2. what path are you loading that yields this result?

--nate

We'll look again at the webpage for more clues. As for trying to reproduce it elsewhere, the data we are using here are all from Galaxy main which has run the jobs several times without a problem. So we're confident we are missing something at our end in the set up - presumably to do with memory usage by TopHat - any thoughts would be most welcome.

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.Matthews@bristol.ac.uk

On 10 Dec 2011, at 14:18, Jeremy Goecks wrote:

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.Matthews@bristol.ac.uk

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