[Bioperl-l] Saving Codeml Output file

Lorenzo Carretero Paulet locarpau at upvnet.upv.es
Mon Aug 29 12:47:13 EDT 2011


Hi all,
I'm running codeml from the PAML package using the corresponding Bioperl
wrapper. I'd like to save the output file as -outfile => 'mlc', as in:
my $codeml_factory = new Bio::Tools::Run::Phylo::PAML::Codeml
						( -outfile => 'mlc',
						-save_tempfiles => 1,
						-alignment => $codon_MSA,
						-tree =>	$biotree,
						-params =>
{
#'outfile' =>'mlc',									'verbose' => 1,									'noisy' => 9,
'runmode' => 0, #user tree
'seqtype' => 1,
'model' => $model,
'NSsites' => $NSsites,
'fix_omega' => $fix_omega,
'omega' => $omega,
'ncatG' => $ncatG,
'icode' => 0, #* 0:universal code; 1:mammalian mt; 2-10:see below (5:ciliate
nuclear)									#'fix_alpha' => 0,								#'fix_kappa' =>
0,							#'RateAncestor' => 0,								'CodonFreq' => 2,								'cleandata' =>
1, # remove sites with amibguity data (1 yes, 0 no),
'ndata' => 1
										},
						);

and subsequently parsing it using
my $parserF= Bio::Tools::Phylo::PAML->new (-file => "mlc", -dir => "./");

However, I get the following message.

------------- EXCEPTION -------------
MSG: Could not open mlc: No such file or directory
STACK Bio::Root::IO::_initialize_io /Library/Perl//5.10.0/Bio/Root/IO.pm:351
STACK Bio::Tools::Phylo::PAML::new
/Library/Perl//5.10.0/Bio/Tools/Phylo/PAML.pm:239
STACK main::BranchSiteEvolAnalysis
/Users/marioafares/Documents/workspace/BactEvolGen/BactEvolGen.pl:1421
STACK toplevel
/Users/marioafares/Documents/workspace/BactEvolGen/BactEvolGen.pl:939
-------------------------------------

what I guess means the output file is not being saved in the previous step.
Anyone knows what's wrong.
Tnak you very much in advance for your help.
Cheers,
Lorenzo


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