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#!/usr/bin/perl

use strict;
...
# do loads of stuff...

my $factory=Bio::Tools::Run::Alignment::TCoffee->new();

Use of uninitialized value $name in pattern match (m//) at /usr/share/
+perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm line 499.

------------- EXCEPTION: Bio::Root::Exception -------------
...
STACK: Bio::Tools::Run::Alignment::TCoffee::new /usr/share/perl5/Bio/T
+ools/Run/Alignment/TCoffee.pm:612
STACK: /home/s0451486/usr/bin/t_coffeeTest.pl:13
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