Re: [Mauve-users] Export GAPS

[Aaron D. <aar...@ut...>]

Hi Cristina, apologies for the late reply, I am trying to get through
the email backlog.
Would you be able to send me the alignment, input sequences, and
.backbone and .bbcols files off-list via google drive or something
similar? It is not obvious to me why you would be getting an empty file
so I would like to try to reproduce the problem on your data and then
step through the code with a debugger.
Best,
-Aaron
On Tue, 2016-09-20 at 16:13 -0300, Cristina Kraemer Zimpel wrote:
> Hi, I am not using the command line (not sure if it run from the
> command as well).
> The version is MAUVE 2.4.0.
> 
> the message in the MAUVE console:
> after the alignment 
> "done.
> root alignment has 84 superintervals
> root alignment length: 4924424
> Organisms have 65.6% GC
> Completed without error.
> Alignment complete!
> set 20, 2016 4:18:13 PM java.util.prefs.WindowsPreferences <init>
> WARNING: Could not open/create prefs root node
> Software\JavaSoft\Prefs at root 0x80000002. Windows
> RegCreateKeyEx(...) returned error code 5."
> 
> 
> 
> 2016-09-20 14:42 GMT-03:00 Joseph Fass <jos...@gm...>:
> > Are you running the export from the GUI? (I'm not sure if there's a
> > way to run it from the command line)
> > Does it give you an error message in the GUI?
> > What build / version of Mauve are you using?
> > 
> > ~Joe
> > 
> > 2016-09-20 7:19 GMT-07:00 Cristina Kraemer Zimpel 
> > l.com>:
> > > 
> > > Hi
> > > 
> > > I performed the progressive alignment with 7 Mycobacterial
> > > genomes, and now I am trying to export gaps, unfortunately when I
> > > choose this option I have as result an empty file.
> > > Can anyone guide me here?
> > > Thank you
> > > -- 
> > > Cristina Kraemer Zimpel
> > > 
> > > Médica Veterinária, Especialista em Medicina Veterinária do
> > > Coletivo 
> > > Mestranda do Departamento de Medicina Veterinária Preventiva e
> > > Saúde Animal (VPS)
> > > Universidade de São Paulo - Faculdade de Medicina Veterinária e
> > > Zootecnia
> > > Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária
> > > São Paulo, SP, CEP 05508 270, Brasil
> > > 
> > > 
> > > ---------------------------------------------------------------
> > > ---------------
> > > 
> > > _______________________________________________
> > > Mauve-users mailing list
> > > Mau...@li...
> > > https://lists.sourceforge.net/lists/listinfo/mauve-users
> > > 
> > 
> > 
> > -- 
> > Joseph Fass
> > Bioinformatics Data Analyst
> > UC Davis Genome Center - Bioinformatics Core
> > http://bioinformatics.ucdavis.edu/
> > jn...@uc...
> > phone ~ 530.752.2698
> > 
> 
> 
> -- 
> Cristina Kraemer Zimpel
> 
> Médica Veterinária, Especialista em Medicina Veterinária do Coletivo 
> Mestranda do Departamento de Medicina Veterinária Preventiva e Saúde
> Animal (VPS)
> Universidade de São Paulo - Faculdade de Medicina Veterinária e
> Zootecnia
> Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária
> São Paulo, SP, CEP 05508 270, Brasil
> 
> -------------------------------------------------------------------
> -----------
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> Mauve-users mailing list
> Mau...@li...
> https://lists.sourceforge.net/lists/listinfo/mauve-users
-- 
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman





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