[Bioperl-l] program bp_pairwise_kaks
Brian Osborne
bosborne11 at verizon.net
Thu Jan 22 19:01:26 UTC 2009
Markus,
"Might the script have some problems in finding the program even the
path is set?"
First I'd make sure that the path _is_ set correctly. If the program
hasn't been installed by Cygwin or compiled from within Cygwin then
you may have to do something like:
setenv ${PATH}:/cygdrive/c/Program Files/clustalw/bin
That refers to C:, of course.
Brian O.
On Jan 22, 2009, at 1:32 PM, Markus Liebscher wrote:
> Hi Brian,
> thanks for helping me. I found it curious that yn00 or codeml are
> looking for their corresponding .ctl files even I set the path
> in .bashrc. Now I am running the programs from within the installed
> paml directory under Cygwin and everything is fine.
> But if I am doing this from a script like bp_pairwise_kaks the
> program seems not to work cause I am getting no results. Might the
> script have some problems in finding the program even the path is set?
> Hope there is an answer.
> Best regards,
> Markus.
>
>
> -------- Original-Nachricht --------
>> Datum: Thu, 22 Jan 2009 12:42:57 -0500
>> Von: Brian Osborne <bosborne11 at verizon.net>
>> An: Markus Liebscher <Markus.Liebscher at gmx.de>, BioPerl List <bioperl-l at lists.open-bio.org
>> >
>> Betreff: Re: [Bioperl-l] program bp_pairwise_kaks
>
>> 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
>>>>>
>>>>
>>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit
> allen: http://www.gmx.net/de/go/multimessenger
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