[Bioperl-l] Building Many trees with Bioperl

[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.



On 24/05/2013 22:25, "Brian Osborne" <bosborne11 at verizon.net> wrote:

>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.
>
>
>On May 24, 2013, at 3:14 PM, Ben Ward (TSL)
><Ben.Ward at sainsbury-laboratory.ac.uk> wrote:
>
>> 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.phyli
>>p  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.phyli
>>p  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.phyl
>>ip_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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>