[Bioperl-l] RE: Problem running clustalw.pl for the first time.

[Scott Cain]

Lisa,

Sorry, I don't know anything about clustal--hopefully that error message
will be meaningful to someone :-)

Scott

On Thu, 2005-04-07 at 05:14 +0100, Lisa wrote:
> Dear Scott,
> Thanks for responding and so quickly.
> I tried as you stated and it worked!!!! 
> However I got the following different error
> Beginning parameter-varying example... 
> Performing alignment with ktuple = 1 
> 
> ------------- EXCEPTION -------------
> MSG: Clustalw call ( align -infile=/tmp/hdhgOZFMXb/SBKpkT1RWy -
> output=gcg -ktuple=1 -outfile=/tmp/hdhgOZFMXb/HpOjRcDK5T >/dev/null
> 2>/dev/null) crashed: 32512 
> 
> STACK
> Bio::Tools::Run::Alignment::Clustalw::_run /home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4//Bio/Tools/Run/Alignment/Clustalw.pm:557
> STACK
> Bio::Tools::Run::Alignment::Clustalw::align /home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4//Bio/Tools/Run/Alignment/Clustalw.pm:473
> STACK main::vary_params clustalw.pl:111
> STACK toplevel clustalw.pl:88
> 
> --------------------------------------
> I am trying to run it all through virtual hosting (with Bio Perl
> installed by host and clustalw complied and running) but I'm not
> running as root. 
> Do you know if this will cause any problems? 
> I am not even able to view the files written to the tmp dir but I can
> tell that they are
> there.http://www.bioplanet.com/planetforums/viewthread.php?tid=2597
> Can you recommend anywhere to find out more info about this and other
> execptions?
> Many Thanks
> Lisa
> 
> 
> Scott Cain wrote:
> > Hi Lisa,
> > 
> > I think you need to shorten your use lib to:
> > 
> > use lib 
> > "/home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4";
> > 
> > Scott
> > 
> > On Thu, 2005-04-07 at 03:40 +0100, Lisa wrote:
> >   
> > > Hello,
> > > 
> > >  I am new to BioPerl and have had the modules installed by our system 
> > > admin (They appear to be installed correctly)
> > > and I have complied the clustalw and it works from cmd line. But I cant 
> > > run clustalw.pl it produces a typical perl error message below :
> > > 
> > > ------------------------------------------------------------
> > > Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: 
> > > /home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4/Bio/Tools/Run/Alignment/ 
> > > /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 
> > > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi 
> > > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi 
> > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi 
> > > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi 
> > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 
> > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 
> > > /usr/lib/perl5/site_perl 
> > > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi 
> > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi 
> > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi 
> > > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi 
> > > /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 
> > > /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 
> > > /usr/lib/perl5/vendor_perl .) at clustalw.pl line 39. BEGIN 
> > > failed--compilation aborted at clustalw.pl line 39.
> > > ------------------------------------------------------------
> > > 
> > > ------------------------------------------------------------
> > > This is the code  from clustalw.pl
> > > ------------------------------------------------------------
> > > #!/usr/bin/perl
> > > 
> > > # PROGRAM  :   
> > > # PURPOSE  : Demonstrate possible uses of 
> > > Bio::Tools::Run::Alignment::Clustalw.pm
> > > # AUTHOR   : Peter Schattner schattner at alum.mit.edu
> > > # CREATED  : Oct 06 2000
> > > # REVISION : $Id: clustalw.pl,v 1.1 2003/07/07 18:20:58 bosborne Exp $
> > > .
> > > 
> > > # Modify (and un-comment) the following line as required to point to 
> > > clustalw program directory on your system
> > > BEGIN {
> > >  $ENV{CLUSTALDIR} = 
> > > '/home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4/Bio/Tools/Run/Alignment/';
> > > }
> > > 
> > > use lib 
> > > "/home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4/Bio/Tools/Run/Alignment/";
> > > use Getopt::Long;
> > > use Bio::Tools::Run::Alignment::Clustalw;
> > > use Bio::SimpleAlign;
> > > use Bio::AlignIO;
> > > use Bio::SeqIO;
> > > use strict;
> > > 
> > > ------------------------------------------------------------
> > > 
> > > 
> > > I would like some information or suggestions for what I can do to get 
> > > this to work.
> > > 
> > > Cheers
> > > Lisa
> > > 
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > > 
> > >     
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory