[Bioperl-l] PAML problem

Du, Peng du at ibio.jp
Tue Jun 26 21:28:00 EDT 2012


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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