[Bioperl-l] PAML problem

Jason Stajich jason.stajich at gmail.com
Tue Jun 26 21:37:55 EDT 2012

Peng -

This module needs a person who's sole job is to keep tracking bugs and updating it with new versions of the program. so far it has burned out several developers on working on it since it not stable. 

I am not sure what the answer is to the problem, but often it depends on the extra parameters used as this changes the order of the output making it hard to parse.

So I don't have a solution for you except that you'll have to post the bug and the problem output mlc file to redmine and hope that we can entice some developers to bang their head against this some more.

On Jun 26, 2012, at 6:28 PM, Du, Peng wrote:

> Hi everyone,
> I am using bioperl to parse paml output, and I saw this
> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> MSG: Unknown format of PAML output did not see seqtype
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::Tools::Phylo::PAML::_parse_summary
> /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:461
> STACK: Bio::Tools::Phylo::PAML::next_result
> /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:270
> STACK: main::cal_dn_ds dn_ds.pl:131
> STACK: dn_ds.pl:44
> ----------------------------------------------------------------
> I googled and found that, it was caused by PAML version
> incompatibility. I tried 3.13, 3.14, 4.1, 4.2, 4.5 and none of them
> worked. Could someone tell me which version is fine?
> My bioperl version is 1.006001.  Thank you very much.
> -- 
> Peng Du
> Graduate School of Information Science and Technology, Hokkaido University
> Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
> Email: du at ibio.jp Tel: +81 80 3268 9713
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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