[Bioperl-l] Building Many trees with Bioperl

[Ben Ward (TSL)]

Hi,

I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
But I need to get it right for one pice of test data before I can do it for all:

What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.

However it gives me many errors like:
--------------------- WARNING ---------------------
MSG: Replacing one sequence [FXCNDTJ02P/1-366]

And then gives me:
Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip 0 i 1 0 HKY e e 1 e BIONJ y y

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip 0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
-----------------------------------------------------------

Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
my $inputfilename = 'outputalignmentfile';
my $tree = $factory->run("$inputfilename");

But I get the same EXCEPTION: Bio::Root::Exception message.

Thanks,
Ben W.

SCRIPT ---

#!/usr/bin/perl
use warnings;
use strict;
BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
use Bio::TreeIO;
use Bio::AlignIO;
use Bio::Tools::Run::Phylo::Phyml;

my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
-format => 'phylip');

my $aln = $alnin->next_aln();


# Make a Phyml factory.
my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
-data_type => 'dna');

# Pass the factory an alignment and run:
# my $inputfilename = 'outputalignmentfile';

my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.


# Setup tree output stream...
my $treeio = Bio::TreeIO->new(-format => 'newick',
-file => 'tree.newick');

$treeio->write_tree($tree);

exit 0;

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[Brian Osborne]

Ben,

What happens when you take the Phyml command itself and run it from the command line?

Also, a minor point: the message "MSG: Replacing one sequence [FXCNDTJ02P/1-366]" is not an error, it is a warning. An error accompanies an exit, warnings are just informative.

Brian O.

[Ben Ward (TSL)]

Hi,

If I just run phyml on the command line it seems to run ok - it accept's
my file and appears to undergo the tree building process - I haven't
actually see it complete yet, but ML and Bayes always does take a while -
and I have many reads that need to be aligned. But PhyML gets to the point
it asks - are you sure you want to proceed - I say yes, then it keeps
quiet and is currently working along to itself:

. 766 patterns found (out of a total of 795 sites).

. 58 sites without polymorphism (7.30%).

. Computing pairwise distances...

. Building BioNJ tree...

. WARNING: this analysis requires at least 556 MB of memory space.

. Do you really want to proceed? [Y/n] Y


It appears to be working =/

Best,
Ben.