[Bioperl-l] Problem with T-Coffee

[Jonathan Manning]

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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