[Bioperl-l] PAML problem

Gahl ahlberg.gustav at gmail.com
Thu Sep 6 11:14:04 EDT 2012


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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