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Old 10-18-2011, 11:55 PM   #1
Ami
Junior Member
 
Location: Singapore

Join Date: Aug 2010
Posts: 6
Default upload error in local instance of galaxy

Hi,

I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to upload a file more that 2 GB in size, the error log is pasted below. I tried to google but it was not of much help.

127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1" 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2"
Debug at: http://127.0.0.1:8080/_debug/view/1319007854
----------------------------------------

Exception happened during processing of request from ('127.0.0.1', 61099)
Traceback (most recent call last):
File "/Users/amit/galaxy-python/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 "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 617, in __init__
self.handle()
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle
BaseHTTPRequestHandler.handle(self)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request
self.wsgi_execute()
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute
self.wsgi_start_response)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 202, in __call__
return app(environ, start_response)
File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__
return self.app( environ, start_response )
File "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py", line 164, in __call__
app_iter = self.application(environ, start_response)
File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__
return self.application(environ, replacement_start_response)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 226, in __call__
return self.respond(environ, start_response)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 399, in respond
if self.xmlhttp_key in req.params:
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 900, in params
params = self.str_params
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST
keep_blank_values=True)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__
self.read_single()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single
self.read_lines()
File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py", line 253, in read_lines
self.read_lines_to_outerboundary()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 467, in readline
data = self.file.readline(self.length - self._consumed)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline
bline = buf.readline(size)
OverflowError: long int too large to convert to int

Please help me to fix this, the python version is 2.6.6. Thank you.

Sincerely,

Amit
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Old 10-19-2011, 04:00 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077
Default

Ami: I hope you are cross-posting this to Galaxy support list. We like to help on SeqAnswers but you are likely to get a more prompt response from Galaxy support.

This may help you with the error: http://gmod.827538.n3.nabble.com/Que....html#a2890156
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Old 10-19-2011, 08:53 AM   #3
Ami
Junior Member
 
Location: Singapore

Join Date: Aug 2010
Posts: 6
Default

Hi

Thanks for the advise, so I posted this in the galaxy support list and got a response from them.

Thank you

Amit
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