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
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
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:
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
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
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:
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
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:
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:
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.Matthews@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 <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.
- is debug = True?
- 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
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:
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:
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.Matthews@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 <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.
- is debug = True?
- 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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David Matthews -
David Matthews
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Jeremy Goecks -
Nate Coraor