[Bioperl-l] Problem with T-Coffee

[Jason Stajich]

different versions of bioperl/bioperl-run on the dev machine and other
machine?  This happens for every every
alignment you try on the non-dev machine? i.e.
% perl -I. -w t/TCoffee.t
in bioperl-run fails on the new machine too?

An example sequence file and the script with at least the t-coffee part
would help in debugging the problem if all of that is true.

I've also moved to using MUSCLE instead of T-Coffee for some analyses
because it is much faster and seems to be as accurate.  The newest MAFFT
is also rumoured to be as accurate too although one should always do their
own tests on one's own data first...

-jason
On Fri, 27 Aug 2004, [iso-8859-1] Jonathan Manning wrote:

> Hi to all,
>
> I've been using T-Coffee via the Bioperl wrapper as
> part of a larger project. Though it worked fine on the
> development system, it's not working on a different
> one. It seems to do the pairwise stuff, at least it
> gets to this stage:
>
> ......
> 	AAH76853  CAG05593 : score=  400
> 	AAH76853  CAE45989 : score=  410
> 	CAG05593  CAE45989 : score=  460
>
>
> MAKE NEIGHBOR JOINING DENDROGRAM
> 	[MODE=fast] [Output dendrogram file=5XIMxfCi1F.dnd]
>
>
> But then it crashes out with the following messages:
>
> Abnormal Program Termination:[T-COFFEE, Version_1.37]
> Please report the fault to:
> cedric.notredame at europe.com (Indicate the version
> number)
> Thank you for your cooperation :-)
>
> ------------- EXCEPTION  -------------
> MSG: TCoffee call crashed: 256 [command
> /usr/bin/t_coffee
> -in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
>  -ktuple=2 -output=clustalw
> -outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]
>
> STACK Bio::Tools::Run::Alignment::TCoffee::_run
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:814
> STACK Bio::Tools::Run::Alignment::TCoffee::align
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:719
> STACK SSIR::align
> /usr/lib/perl5/site_perl/5.8.0/SSIR.pm:2094
> STACK toplevel /var/www/cgi-bin/ssir.cgi:557
>
> --------------------------------------
>
> Similar commands work fine from the command line.
>
> Does anyone have any ideas?
>
> Many thanks,
>
> Jon
>
>
>
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu