[Bioperl-l] I can't access clustalw from my cgi perl program...

nisa_dar vdar at yorku.ca
Thu May 22 14:23:45 EDT 2008


this is from my error log file, does this make any sense to anyone in order
to help me out

[Thu May 22 14:20:01 2008] [error] [client ] STACK: Error::throw, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:01 2008] [error] [client ] STACK: Bio::Root::Root::throw
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:328, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:01 2008] [error] [client ] STACK:
Bio::Root::IO::_initialize_io
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Root/IO.pm:313, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:01 2008] [error] [client ] STACK:
Bio::AlignIO::_initialize
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/AlignIO.pm:379, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:01 2008] [error] [client ] STACK: Bio::AlignIO::new
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/AlignIO.pm:305, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:01 2008] [error] [client ] STACK: Bio::AlignIO::new
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/AlignIO.pm:326, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:01 2008] [error] [client ] STACK:
/export/share/iNquiry/www/cgi-bin/bipod/nisa/snpfinder.cgi:64, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:01 2008] [error] [client ]
-----------------------------------------------------------, referer:
https://capsella.ccs.yorku.ca/nisa/snp_finder.html
[Thu May 22 14:20:02 2008] [error] [client ] File does not exist:
/var/www/html/favicon.ico
[Thu May 22 14:20:04 2008] [error] [client ] File does not exist:
/var/www/html/favicon.ico




Thanks









Dave Messina-3 wrote:
> 
> Since your script runs correctly from the command line, this doesn't look
> like it's a BioPerl problem.
> 
> The error message you got is:
> 
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm
> 
> 
> followed by a long list of directories where it looked for that module. So
> the first thing to check is
> 
> Is Bio/Tools/Run/Alignment/Clustalw.pm in one of those @INC directories?
> 
> The fact that other Bioperl modules are 'use'd in your script first and
> didn't produce an error suggests that you might have the BIoperl core
> installation in those directories, but not Bio::Tools::Run.
> 
> If Bio/Tools/Run/Alignment/Clustalw.pm is in fact in the @INC directories
> listed, then it's probably a CGI/web issue. Do you know as what user on
> your
> machine web scripts are run? That user probably has limited permissions
> compared to your regular user account.
> 
> 
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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