Hi Aleksander,
There appears to be a bug in the SNP exporter, wherein it fails to
write the last part of the output. I have just committed a fix to the
source code repository:
https://sourceforge.net/p/mauve/code/4736/
I also posted a copy of the updated jar file into a repository for an
unrelated project:
https://github.com/cerebis/meta-sweeper/blob/multisample/external/mauve
_snapshot_2015-02-13/Mauve.jar?raw=true
If you can replace the Mauve.jar on your computer with that one it
should hopefully resolve the problem, but do let us know if the issue
persists.
Best,
-Aaron
On Wed, 2016-06-08 at 10:11 +0200, Aleksander Mahnič wrote:
> Greetings Mauve community,
>
> I have a small problem with extracting SNPs from our Mauve alignment.
>
> We have a set of 50 genomes (same species but quite diverse). When
> extracting SNPs
> from s subset alignment (15 genomes) it works perfectly, but when I
> include all genomes,
> the output file remains empty.
>
> Doesn't seem to be lack of CPU or memory and I let it run for almost
> 12 hours.
>
> Do you have any experience with such problem?
> Are there other ways to extract SNPs from Mauve alignment?
>
> Thank you for any help you can provide.
>
> Best regards,
>
> Aleksander
>
> --
> The National Laboratory of Health, Environment and Food (NLZOH)
> Prvomajska ulica 1, 2000 Maribor, Slovenia
> tel: +386 (0)2 4500 175
> -------------------------------------------------------------------
> -----------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and
> protocols are
> consuming the most bandwidth. Provides multi-vendor support for
> NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using
> capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659
> 582;e
> _______________________________________________
> Mauve-users mailing list
> Mauve-users@lists.sourceforge.net
> 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.
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
