[Bioperl-l] program bp_pairwise_kaks

Thu Jan 22 17:42:57 UTC 2009

Markus,

I don't know the answer, and I don't know if this helps you but if  
you're trying to use some application or resource outside of Cygwin  
directory or you're having a problem remember that Cygwin's path  
syntax may not be the correct one. Cygwin understands /home/jacky or / 
cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the  
external resource may want E:/cygwin/home/jacky. So your files may end  
up as paths written in these different syntaxes, depending on what the  
app is, how it was compiled, and so on.

For example, for some apps and Cygwin, I had to set $TMPDIR like this:

setenv TMPDIR C:/cygwin/tmp

Brian O.

On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote:

> I would see if anyone on list can help I don't know what windows  
> issues there  might be. You can write some test scripts to verify  
> that codeml can be found via the executeable method (past list  
> postings discuss this) and you can make sure the test in bioperl-run  
> pass for PAML.
>
> Sent from my iPod
>
> On Jan 22, 2009, at 6:49 AM, Markus Liebscher  
> <Markus.Liebscher at gmx.de> wrote:
>
>> Hi Jason,
>> sorry for bothering you again. But I don't get this...
>> I got the installation of PAML done under Cygwin. But now I am a  
>> little bit confused. I added the PATH as suggested in the  
>> installation routine then switched to where the data file of yn00  
>> and codeml is (in my case /home/Markus/paml42) and run the following:
>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml
>>
>> giving me the output:
>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml
>>
>> CLUSTAL W (1.82) Multiple Sequence Alignments
>>
>> Sequence format is Pearson
>> Sequence 1: CBG10100        363 aa
>> Sequence 2: F22B7.13        525 aa
>> Sequence 3: C38C10.4        525 aa
>> Start of Pairwise alignments
>> Aligning...
>> Sequences (1:2) Aligned. Score:  9
>> Sequences (1:3) Aligned. Score:  8
>> Sequences (2:3) Aligned. Score:  96
>> Guide tree        file created:   [/tmp/YFogrzX7C4/14pjJGZx8t.dnd]
>> Start of Multiple Alignment
>> There are 2 groups
>> Aligning...
>> Group 1: Sequences:   2      Score:11215
>> Group 2:                     Delayed
>> Sequence:1     Score:2745
>> Alignment Score 3187
>> GCG-Alignment file created      [/tmp/YFogrzX7C4/ccVi5EKuvw]
>> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty  
>> at /usr/lib/perl5/site_perl/5.10/Bi
>> o/Tools/Run/WrapperBase.pm line 243
>> SEQ1    SEQ2    Ka      Ks      Ka/Ks   PROT_PERCENTID   
>> CDNA_PERCENTID
>>
>> But when I run
>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00
>>
>> I get this:
>> CLUSTAL W (1.82) Multiple Sequence Alignments
>>
>>
>>
>> Sequence format is Pearson
>> Sequence 1: CBG10100        363 aa
>> Sequence 2: F22B7.13        525 aa
>> Sequence 3: C38C10.4        525 aa
>> Start of Pairwise alignments
>> Aligning...
>> Sequences (1:2) Aligned. Score:  9
>> Sequences (1:3) Aligned. Score:  8
>> Sequences (2:3) Aligned. Score:  96
>> Guide tree        file created:   [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd]
>> Start of Multiple Alignment
>> There are 2 groups
>> Aligning...
>> Group 1: Sequences:   2      Score:11215
>> Group 2:                     Delayed
>> Sequence:1     Score:2745
>> Alignment Score 3187
>> GCG-Alignment file created      [/tmp/0iEr4jig5Z/sHPCpKTXc7]
>> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty  
>> at /usr/lib/perl5/site_perl/5.10/Bi
>> o/Tools/Run/WrapperBase.pm line 243
>> Use of uninitialized value in pattern match (m//) at /usr/bin/ 
>> bp_pairwise_kaks.pl line 182, <GEN2> l
>> ine 101.
>> SEQ1    SEQ2    Ka      Ks      Ka/Ks   PROT_PERCENTID   
>> CDNA_PERCENTID
>> F22B7.13        C38C10.4        0.0167  0.0310  0.5370  96.95   97.78
>> F22B7.13        CBG10100        1.7712  2.5286  0.7005  16.25   35.08
>> C38C10.4        CBG10100        1.8658  2.4364  0.7658  15.43   34.53
>>
>> What I've made wrong with, that I can't use codeml? And where is my  
>> final alignment gone?
>> Any help is deeply appreciated.
>> Best regards,
>> Markus.
>>
>>
>>
>> Jason Stajich wrote:
>>> Markus-
>>>
>>> You need to have also installed PAML in order to do the  
>>> calculation with PAML.  There is example code on the HOWTOs for  
>>> running the perl-only Ka/Ks counts methods that are in  
>>> Bio::Align::DNAStatistics
>>> Jason Stajich
>>> jason at bioperl.org <mailto:jason at bioperl.org>
>>> http://bioperl.org/wiki/User:Jason
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: *Markus Liebscher* <Markus.Liebscher at gmx.de <mailto:Markus.Liebscher at gmx.de 
>>> >>
>>> Date: Tue, Jan 20, 2009 at 6:22 AM
>>> Subject: program bp_pairwise_kaks
>>> To: jason at bioperl.org <mailto:jason at bioperl.org>
>>>
>>>
>>> Dear Jason,
>>> I found the Bioperl package very useful. But I failed to run the  
>>> bp_pairwise_kaks program.
>>> I tried to run bp_pairwise_kaks as suggested using the command  
>>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna.
>>> The program starts the routine but at the end I get this:
>>>
>>> --------------------------------------------------------
>>> CLUSTAL W (1.82) Multiple Sequence Alignments
>>> Sequence format is Pearson
>>> Sequence 1: CBG10100        363 aa
>>> Sequence 2: F22B7.13        525 aa
>>> Sequence 3: C38C10.4        525 aa
>>> Start of Pairwise alignments
>>> Aligning...
>>> Sequences (1:2) Aligned. Score:  9
>>> Sequences (1:3) Aligned. Score:  8
>>> Sequences (2:3) Aligned. Score:  96
>>> Guide tree        file created:   [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd]
>>> Start of Multiple Alignment
>>> There are 2 groups
>>> Aligning...
>>> Group 1: Sequences:   2      Score:11215
>>> Group 2:                     Delayed
>>> Sequence:1     Score:2745
>>> Alignment Score 3187
>>> GCG-Alignment file created      [/tmp/5M8igBfS6R/JI0anpGzWn]
>>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty  
>>> at /usr/lib/perl5/site_perl/5.10/Bi
>>> o/Tools/Run/WrapperBase.pm line 243
>>> SEQ1    SEQ2    Ka      Ks      Ka/Ks   PROT_PERCENTID   
>>> CDNA_PERCENTID
>>> --------------------------------------------------------
>>>
>>> Do you have an idea what happened here and how I can solve this  
>>> problem? I appreciate any help with this.
>>> I am running Cygwin under Windows XP, and have installed clustalw,  
>>> t-coffee, the bioperl package and the bioperl package run with the  
>>> "Build" scripts.
>>>
>>> Best regards,
>>> Markus.
>>>
>>> Dr. Markus Liebscher
>>> Martin-Luther-University Halle/Wittenberg
>>> Dept. Natural product chemistry
>>> Kurt-Mothes-Str.3
>>> 06120 Halle (Saale)
>>> Germany
>>>
>>
>>
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