Hi,

On my local galaxy installation (updated to the latest version yesterday), it takes ages  (hours!) to upload a fastq files. I attach a report from the the computer on which galaxy is installed. The fastq file is uploaded from
132.72.88.186. Initially there is an error message (the attached file also includes the debug url at the end) and after a while the upload proceeds but takes very long time. Transferring the file by sftp between the two computers takes only seconds.
Is there anytning wrong with my installation (i.e. something is not properly defined or something like this).

I'd appreciate your help.

                     Boaz
 
Boaz Shaanan, Ph.D.                                        
Dept. of Life Sciences                                     
Ben-Gurion University of the Negev                         
Beer-Sheva 84105                                           
Israel                                                     
                                                           
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan                 
Fax:   972-8-647-2992 or 972-8-646-1710    
 
 
                

/home/bshaanan/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215:
 SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects 
natively, and SQLAlchemy must convert from floating point - rounding errors and 
other issues may occur. Please consider storing Decimal numbers as strings or 
integers on this platform for lossless storage.                                 
                                                                                
                          
132.72.88.186 - - [14/Aug/2013:13:32:45 +0300] "GET / HTTP/1.1" 200 - "-" 
"Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"          
                                                                                
                                                    
132.72.88.186 - - [14/Aug/2013:13:32:52 +0300] "GET /root/welcome HTTP/1.1" 302 
- "http://dylan.bgu.ac.il:8082/"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                                                   
132.72.88.186 - - [14/Aug/2013:13:32:52 +0300] "GET /history HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                                                        
132.72.88.186 - - [14/Aug/2013:13:32:58 +0300] "GET 
/history/get_display_application_links HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/history"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                   
132.72.88.186 - - [14/Aug/2013:13:33:18 +0300] "GET /user/login HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                                                     
132.72.88.186 - - [14/Aug/2013:13:33:29 +0300] "POST 
/user/login?use_panels=False HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/user/login"; "Mozilla/5.0 (X11; Linux x86_64; 
rv:20.0) Gecko/20100101 Firefox/20.0"                                           
                                  
/home/bshaanan/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
 SAWarning: The IN-predicate on "request_type.id" was invoked with an empty 
sequence. This results in a contradiction, which nonetheless can be expensive 
to evaluate.  Consider alternative strategies for improved performance.         
                                                                             
132.72.88.186 - - [14/Aug/2013:13:33:30 +0300] "GET / HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/user/login?use_panels=False"; "Mozilla/5.0 (X11; 
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"                             
                                                           
132.72.88.186 - - [14/Aug/2013:13:33:30 +0300] "GET /root/welcome HTTP/1.1" 302 
- "http://dylan.bgu.ac.il:8082/"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                                                   
132.72.88.186 - - [14/Aug/2013:13:33:30 +0300] "GET /history HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                                                        
132.72.88.186 - - [14/Aug/2013:13:33:31 +0300] "GET 
/history/get_display_application_links HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/history"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                   
132.72.88.186 - - [14/Aug/2013:13:34:23 +0300] "GET 
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://dylan.bgu.ac.il:8082/"; 
"Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"          
                                                                              
132.72.88.186 - - [14/Aug/2013:13:37:25 +0300] "POST 
/tool_runner/upload_async_create HTTP/1.1" 200 - "http://dylan.bgu.ac.il:8082/"; 
"Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"          
                                                                         
132.72.88.186 - - [14/Aug/2013:13:37:26 +0300] "GET 
/tool_runner/upload_async_message HTTP/1.1" 200 - 
"http://dylan.bgu.ac.il:8082/"; "Mozilla/5.0 (X11; Linux x86_64; rv:20.0) 
Gecko/20100101 Firefox/20.0"                                                    
                               
132.72.88.186 - - [14/Aug/2013:13:37:26 +0300] "POST /tool_runner/index 
HTTP/1.1" 500 - "http://dylan.bgu.ac.il:8082/tool_runner?tool_id=upload1"; 
"Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"          
                                                            
Debug at: http://dylan.bgu.ac.il:8082/_debug/view/1376476017                    
                                                               
----------------------------------------                                        
                                                               
Exception happened during processing of request from ('132.72.88.186', 43962)   
                                                               
Traceback (most recent call last):                                              
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
 line 1068, in process_request_in_thread           
    self.finish_request(request, client_address)                                
                                                               
  File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request      
                                                               
    self.RequestHandlerClass(request, client_address, self)                     
                                                               
  File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__            
                                                               
    self.handle()                                                               
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
 line 442, in handle                               
    BaseHTTPRequestHandler.handle(self)                                         
                                                               
  File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle            
                                                               
    self.handle_one_request()                                                   
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
 line 437, in handle_one_request                   
    self.wsgi_execute()                                                         
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
 line 287, in wsgi_execute                         
    self.wsgi_start_response)                                                   
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py",
 line 203, in __call__                                 
    return app(environ, start_response)                                         
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/request_id.py",
 line 12, in __call__                             
    return self.app( environ, start_response )                                  
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
 line 21, in __call__                         
    return self.app( environ, start_response )                                  
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
 line 68, in __call__                            
    return self.application(environ, replacement_start_response)                
                                                               
  File 
"/home/bshaanan/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py",
 line 226, in __call__            
    return self.respond(environ, start_response)                                
                                                               
  File 
"/home/bshaanan/galaxy/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 
"/home/bshaanan/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
 line 900, in params
    params = self.str_params
  File 
"/home/bshaanan/galaxy/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 
"/home/bshaanan/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
 line 818, in str_POST
    keep_blank_values=True)
  File "/usr/lib64/python2.6/cgi.py", line 508, in __init__
    self.read_multi(environ, keep_blank_values, strict_parsing)
  File "/usr/lib64/python2.6/cgi.py", line 635, in read_multi
    headers = rfc822.Message(self.fp)
  File "/usr/lib64/python2.6/rfc822.py", line 108, in __init__
    self.readheaders()
  File "/usr/lib64/python2.6/rfc822.py", line 155, in readheaders
    line = self.fp.readline()
  File 
"/home/bshaanan/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
 line 482, in readline
    data = self.file.readline(max_read)
  File "/usr/lib64/python2.6/socket.py", line 415, in readline
    bline = buf.readline(size)
OverflowError: signed integer is greater than maximum

-------------------------------------------------------------------
------------------------------------------------------------------
Debug at: http://dylan.bgu.ac.il:8082/_debug/view/1376476017

Error Traceback:
View as:   Interactive  |  Text  |  XML (full)
⇝ OverflowError: signed integer is greater than maximum
URL: http://dylan.bgu.ac.il:8082/tool_runner/index
Module weberror.evalexception.middleware:364 in respond         view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__         view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__         view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__         view
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:185 in handle_request         view
>>  kwargs = trans.request.params.mixed()
Module webob:900 in params         view
>>  params = self.str_params
Module webob:892 in str_params         view
>>  return NestedMultiDict(self.str_GET, self.str_POST)
Module webob:818 in str_POST         view
>>  keep_blank_values=True)
Module cgi:508 in __init__         view
>>  self.read_multi(environ, keep_blank_values, strict_parsing)
Module cgi:635 in read_multi         view
>>  headers = rfc822.Message(self.fp)
Module rfc822:108 in __init__         view
>>  self.readheaders()
Module rfc822:155 in readheaders         view
>>  line = self.fp.readline()
Module paste.httpserver:482 in readline         view
>>  data = self.file.readline(max_read)
Module socket:415 in readline         view
>>  bline = buf.readline(size)
OverflowError: signed integer is greater than maximum


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