[Bioperl-l] problem with neighbor.pm

[Elizabeth Williams]

Hello,

I am trying to run the phylip modules on a set of Bio::seq sequences.  I 
have run into a problem with neighbor.pm  The module runs the program but 
then loses the tree somehow and comes up with this error message.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: neighbor did not create tree correctly (expected /tmp/lHCvy7ByeN/treefile)
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/biol/programs/perl580/lib/site_perl/5.8.0/Bio/Root/Root.pm:328
STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::_run 
/biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:412
STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::run 
/biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:353
STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::create_tree 
/biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:370
STACK: geneorigin.pl:74
-----------------------------------------------------------

The script I am using is below.
Anyone have any ideas what is causing the problem?  I am at a loss.

use Bio::DB::GenPept;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::Tools::Run::Phylo::Phylip::ProtDist;
use Bio::Tools::Run::Phylo::Phylip::Neighbor;

#use strict;
use Bio::SeqIO;
use Bio::Seq;
use Bio::AlignIO;
use Bio::SimpleAlign;

$ENV{PHYLIPDIR} = '/biol/programs/phylip/exe';
.
.
.
.
.
.
                         my @params_align = ('ktuple' => 2, 'matrix' => 
'BLOSUM');
                         my $factory = 
Bio::Tools::Run::Alignment::Clustalw->new(@params_align);
                         my $seq_array_ref = \@seq_array; # where 
@seq_array is an array of Bio::Seq objects created earlier
                         my $aln = $factory->align($seq_array_ref);
                         my @params_protdist = ('MODEL' => 'PAM');

                         my $protdist_factory = 
Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params_protdist);

                         my $matrix = $protdist_factory->run($aln);

                         my @params_neighbor = ('type'=>'NJ');



                         my $neighborfactory = 
Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params_neighbor);

                         my $tree = $neighborfactory->create_tree($matrix);


Elizabeth J.B. Williams