Re: [Mauve-users] SNP extraction

[Aleksander M. <ale...@nl...>]

Hi,

It worked perfectly from the command line.

If the following information will be in any help:
I'm running the latest snapshot of Mauve. When working with viewer no error messages appeared in terminal, 
the log window in viewer did not open. Mauve created a bunch of java jobs and ran them on all available 
cores and then just stopped after a few minutes with the output remaining empty.

Thank you for your help.

Best,
Aleksander



----- Izvirno sporočilo -----
Od: "aaron darling" <aar...@ut...>
Za: "mauve-users" <mau...@li...>
Poslano: Torek, 13. December 2016 16:05:28
Zadeva: Re: [Mauve-users] SNP extraction

Hi Aleksander,
No the guide tree is not used in the SNP extraction. Did your
progressiveMauve run generate the .backbone and .bbcols files?
Are you generating the SNP file from the command line or within the
viewer? Are there any messages in either the terminal or the console
log window?
Best,
-Aaron
On Tue, 2016-12-13 at 15:07 +0100, Aleksander  Mahnič wrote:
> Hi all,
> 
> I have some problems with SNP extraction from alignment of 48 genomes
> (the output file remains empty).
> I noticed, that we did not set the progressiveMauve to save the guide
> tree. Could this play a role in SNP extract failing?
> 
> If so.. Is there a fast option to make a guide tree from the
> alignment or is it easier to just run alignment again?
> 
> Thank you.
> 
> Best,
> Aleksander
> 
> -- 
> National Laboratory of Health, Environment and Food (NLZOH)
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-- 
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman





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