Re: [Mauve-users] Export GAPS
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koadman
From: Aaron D. <aar...@ut...> - 2016-10-04 13:31:05
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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 > > ------------------------------------------------------------------- > ----------- > _______________________________________________ > 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 UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |