Hello,
I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens.
File "/home/lin/public_html/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 "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum ---------------------------------------- 127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - " http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2"
What could be going wrong?
Thanks.
Lin
Hello,
I am resending this since it seemed to have gotten lost in the moderation queue somewhere.
I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens.
File "/home/lin/public_html/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 "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum ---------------------------------------- 127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - " http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2"
==== End of error output===
What could be going wrong?
Thanks. Any help would be appreciated. Lin
Hi Linda,
Do you have 'debug = False' in your configuration?
Thanks, --nate
Linda Barnum wrote:
Hello,
I am resending this since it seemed to have gotten lost in the moderation queue somewhere.
I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens.
File "/home/lin/public_html/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 "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum
127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2"
==== End of error output===
What could be going wrong?
Thanks. Any help would be appreciated. Lin
galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Nate,
No, debug is set to true. Some lines from the universe_wsgi.ini file
# Configuration for debugging middleware debug = True use_lint = False
# Interactive debugging - NEVER enable this on a public site use_interactive = True
Lin
On 4/26/10, Nate Coraor nate@bx.psu.edu wrote:
Hi Linda,
Do you have 'debug = False' in your configuration?
Thanks, --nate
Linda Barnum wrote:
Hello,
I am resending this since it seemed to have gotten lost in the moderation queue somewhere.
I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens.
File "/home/lin/public_html/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 "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum
127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2"
==== End of error output===
What could be going wrong?
Thanks. Any help would be appreciated. Lin
galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Lin,
Please try the following:
debug = False use_lint = False use_interactive = False
And let us know if this fixes it for you.
Thanks, --nate
Linda Barnum wrote:
Nate,
No, debug is set to true. Some lines from the universe_wsgi.ini file
# Configuration for debugging middleware debug = True use_lint = False
# Interactive debugging - NEVER enable this on a public site use_interactive = True
Lin
On 4/26/10, Nate Coraor nate@bx.psu.edu wrote:
Hi Linda,
Do you have 'debug = False' in your configuration?
Thanks, --nate
Linda Barnum wrote:
Hello,
I am resending this since it seemed to have gotten lost in the moderation queue somewhere.
I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens.
File "/home/lin/public_html/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 "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum
127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2"
==== End of error output===
What could be going wrong?
Thanks. Any help would be appreciated. Lin
galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Nate,
Thanks, I'll try that out and let you know. In the meanwhile I found that if I use Firefox it seems to work without issues, I was initially using Google Chrome as my browser.
Thanks, Lin
On 4/27/10, Nate Coraor nate@bx.psu.edu wrote:
Hi Lin,
Please try the following:
debug = False use_lint = False use_interactive = False
And let us know if this fixes it for you.
Thanks, --nate
Linda Barnum wrote:
Nate,
No, debug is set to true. Some lines from the universe_wsgi.ini file
# Configuration for debugging middleware debug = True use_lint = False
# Interactive debugging - NEVER enable this on a public site use_interactive = True
Lin
On 4/26/10, Nate Coraor nate@bx.psu.edu wrote:
Hi Linda,
Do you have 'debug = False' in your configuration?
Thanks, --nate
Linda Barnum wrote:
Hello,
I am resending this since it seemed to have gotten lost in the moderation queue somewhere.
I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens.
File "/home/lin/public_html/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 "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum
127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2"
==== End of error output===
What could be going wrong?
Thanks. Any help would be appreciated. Lin
galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Nate,
Your solution did not work. If I use debug=False, on executing the 'get data' tool I get an Internal server error in the right panel. I thought using Firefox worked but it only removed the error from the log that I copied, the file still did not upload.
At this point, what worked was gzipping the qual files and then uploading them. This made them about 2 GB in size and things went smoothly.
-Lin
On Tue, Apr 27, 2010 at 7:26 PM, Linda Barnum lin.barnum@gmail.com wrote:
Nate,
Thanks, I'll try that out and let you know. In the meanwhile I found that if I use Firefox it seems to work without issues, I was initially using Google Chrome as my browser.
Thanks, Lin
On 4/27/10, Nate Coraor nate@bx.psu.edu wrote:
Hi Lin,
Please try the following:
debug = False use_lint = False use_interactive = False
And let us know if this fixes it for you.
Thanks, --nate
Linda Barnum wrote:
Nate,
No, debug is set to true. Some lines from the universe_wsgi.ini file
# Configuration for debugging middleware debug = True use_lint = False
# Interactive debugging - NEVER enable this on a public site use_interactive = True
Lin
On 4/26/10, Nate Coraor nate@bx.psu.edu wrote:
Hi Linda,
Do you have 'debug = False' in your configuration?
Thanks, --nate
Linda Barnum wrote:
Hello,
I am resending this since it seemed to have gotten lost in the moderation queue somewhere.
I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens.
File
"/home/lin/public_html/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 "/usr/lib/python2.6/site-packages/paste/httpserver.py", line
476,
in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum
127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200
"http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2"
==== End of error output===
What could be going wrong?
Thanks. Any help would be appreciated. Lin
galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
galaxy-user@lists.galaxyproject.org
-
Linda Barnum -
Nate Coraor