Re: [galaxy-dev] Galaxy web interface falls over when running TopHat
Hi,
Thanks for the feedback. We are going to try debug=True (it was set to False)
and get back to you. Our latest traceback is listed below...
Exception happened during processing of request from ('xxx.xxx.xxx.xxx', 59168)
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
data = self._sock.recv(self._rbufsize)
MemoryError
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
On 12 Dec 2011, at 21:28, Nate Coraor wrote:
> 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 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: 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
>> line
Re: [galaxy-dev] Galaxy web interface falls over when running TopHat
Hi,
We've just re run a Tophat run with debug=true and this is the email I got back
from our HPC guys:
For the instance that just crashed I ran it interactively i.e. not in daemon
mode and with debug = True
The only error I'm seeing on the screen is:
./run.sh: line 48: 8705 Segmentation fault python ./scripts/paster.py
serve universe_wsgi.ini $@
So we are not much wiser here. As for the question about what path are loading
- sorry for being a bit slow but what exactly do you mean by that?
Sorry we are eating up so much of your time...
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
On 12 Dec 2011, at 21:28, Nate Coraor wrote:
> 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 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: 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
Re: [galaxy-dev] Galaxy web interface falls over when running TopHat
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 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: 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.matth...@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
Re: [galaxy-dev] Galaxy web interface falls over when running TopHat
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 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: 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
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.matth...@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
Re: [galaxy-dev] Galaxy web interface falls over when running TopHat
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 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 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/
___
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/
[galaxy-dev] Galaxy web interface falls over when running TopHat
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 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 >
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/
