For help !!

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For help !!

zhang yancong

   Why my Gbrowse cannot work?  Does anyone know this?

   Here is the error log:

  [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Odd number of elements in hash assignment at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 34, <DATA> line 192
  [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in list assignment at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 34, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in string eq at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 93, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in string eq at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 97, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client  127.1.1.1] Use of uninitialized value in pattern match (m//) at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 98, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in string eq at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 99, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] unknown lock type  at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 137, <DATA> line 192.
  [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Premature end of script headers: gbrowse
  [Mon Jan 13 22:43:57 2014] [error] [client 127.1.1.1] Use of uninitialized value in exists at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2.pm line 408, <DATA> line 192.

Thanks a lot!
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Re: For help !!

Scott Cain
Hi Zhang,

Several questions:

1. What version of GBrowse do you have?

2. How did you install it?  Where there any errors during the installation?

3. Does the sample yeast data that came with GBrowse work?

4. Are you sure the prerequisites installed correctly?  Specifically to start, is CGI::Session installed correctly? (I ask because the first error you posted is in a section of code using CGI::Session).

5. If the yeast data is working, can you please send your configuration file that isn't working, as well as a sample of the GFF that you're using.

Scott



On Mon, Jan 13, 2014 at 8:05 AM, zhang yancong <[hidden email]> wrote:

   Why my Gbrowse cannot work?  Does anyone know this?

   Here is the error log:

  [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Odd number of elements in hash assignment at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 34, <DATA> line 192
  [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in list assignment at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 34, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in string eq at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 93, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in string eq at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 97, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client  127.1.1.1] Use of uninitialized value in pattern match (m//) at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 98, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Use of uninitialized value in string eq at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 99, <DATA> line 192.
 [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] unknown lock type  at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2/Session.pm line 137, <DATA> line 192.
  [Mon Jan 13 22:43:53 2014] [error] [client 127.1.1.1] Premature end of script headers: gbrowse
  [Mon Jan 13 22:43:57 2014] [error] [client 127.1.1.1] Use of uninitialized value in exists at /opt/lib/perl5/site_perl/5.8.9/x86_64-linux/Bio/Graphics/Browser2.pm line 408, <DATA> line 192.

Thanks a lot!
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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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