[Bioperl-l] Phylip error

Jonathan Manning bmb9jrm at bmb.leeds.ac.uk
Wed Jun 2 09:43:18 EDT 2004

Hi to all,

I'm trying to incorporate phylogenetic analysis into a script I'm
writing. I'm attempting to feed in alignments (SimpleAlign objects)
derived from an earlier subroutine, and stored in a global hash (the
reason for the hash being that I wanted to reference by a blast query
sequence). My code:

sub phylip{

	foreach my $key (keys %alignments){
		my ($alnmnt) = $alignments{$key};
		my @params = ('MODEL' => 'PAM');
		my $protdist = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
  		my $matrix  = $protdist->run($alnmnt);
		@params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1,

  		my $neighbor =
		my ($tree) = $neighbor_factory->run($matrix);

It seems to have a problem at the protdist stage, resulting in the
following error:

------------- EXCEPTION  -------------
MSG: protdist did not create matrix correctly (/tmp/q4lIZVPNvW/outfile)
STACK Bio::Tools::Run::Phylo::Phylip::ProtDist::_run
STACK Bio::Tools::Run::Phylo::Phylip::ProtDist::run
STACK main::phylip ./GeneInfo5.pl:1648
STACK toplevel ./GeneInfo5.pl:563

>From the archives, this would seem to be a problem with writing the
matrix to file, but I don't know why. The permissions on /tmp are fine.

Does anyone have any ideas?

Thanks in advance,


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