[Bioperl-l] PAML problem

Fields, Christopher J cjfields at illinois.edu
Tue Sep 11 21:33:33 EDT 2012


Gahl,

Daisie fixed PAML in the latest bioperl-live:

    https://github.com/bioperl/bioperl-live

You can use git to check it out and use it, or use https://github.com/bioperl/bioperl-live/downloads and download a tarball/zip.

chris

On Sep 6, 2012, at 10:14 AM, Gahl <ahlberg.gustav at gmail.com>
 wrote:

> 
> Hello,
> I have the sam problem. How did you fix it?
> 
> Du, Peng wrote:
>> 
>> Hi Daisie,
>> 
>> Problem got fixed~~
>> Thank you ^_^.
>> 
>> On Tue, Sep 4, 2012 at 8:05 PM, Du, Peng <du at ibio.jp> wrote:
>>> Hi Daisie,
>>> 
>>> Thank you for your reply.
>>> Where could I get the bioperl-live you mentioned? Is it something
>>> equivalent to bioperl core package?
>>> If it is, do I need to reinstall the whole bioperl package?
>>> 
>>> Thank you.
>>> Peng
>>> 
>>> On Fri, Aug 17, 2012 at 3:38 AM, Daisie Huang <daisieh at gmail.com> wrote:
>>>> I'm not sure which PAML component caused this particular outcome, but
>>>> the
>>>> bugs and fixes I pushed to bioperl-live might fix this. When will those
>>>> get
>>>> pulled into the master?
>>>> 
>>>> If those particular fixes don't help, I'd be happy to take a peek at the
>>>> originator's code and see if it's a quick re-parsing fix.
>>>> 
>>>> Daisie
>>>> 
>>>> 
>>>> On Tuesday, June 26, 2012 6:37:55 PM UTC-7, Jason Stajich wrote:
>>>>> 
>>>>> 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.
>>>>> 
>>>>> Jason
>>>>> 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: d... at ibio.jp Tel: +81 80 3268 9713
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Biop... at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>>> Jason Stajich
>>>>> jason.... at gmail.com
>>>>> ja... at bioperl.org
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Biop... at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> 
>>> --
>>> 
>>> 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
>> 
>> 
>> 
>> -- 
>> 
>> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> -- 
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