[Bioperl-l] Saving Codeml Output file

Dave Messina David.Messina at sbc.su.se
Mon Aug 29 13:43:33 EDT 2011

Hi Lorenzo,

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

> what I guess means the output file is not being saved in the previous step.

Your interpretation could be correct. I think though that it might be that
the -dir parameter you specify, "./", is not correct. Are you seeing the mlc
file in the '.' (current working) dir?

If I remember correctly, by default the mlc file is created in a temporary
directory in /scratch or /tmp, and the save_tempfiles flag simply keeps that
temporary directory from being deleted.

I don't have the docs in front of me, but I believe there's a way to get the
path of the temp directory that B::T::P::PAML is using. If so, you can use
that path as the value for the -dir parameter.

Let me know if not, though, and we can follow up on this.


PS - also, could you verify that you're using the latest versions of
bioperl-live and bioperl-run from Github?

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