Hi LiXiang,
The time complexity of the progressiveMauve algorithm scales at least
cubically in the number of genomes being aligned, with length being an
additional approximately n log n factor. In practice that means that
the upper limit for progressiveMauve is usually datasets of around 30-
50 bacterial genomes. It should finish if you continue to wait, but you
may be waiting a very long time. Depending on your analysis goals one
option may be to reduce the set of input genomes. Do you need pan-
genome alignment or just core genome alignment? If a core genome
alignment is sufficient for your subsequent analysis tasks, you might
have a look at the Harvest tools (parsnp, gingr) by Treangen et al.
Best,
-Aaron
On Sun, 2016-10-16 at 17:04 +0800, LiXiangchen wrote:
> Hi all,
>
> I used to run progressiveMauve with 49 bacterial genomes, each genome
> is about 13MB. The job has been running for three weeks and is still
> running now. Since I just use all default parameters, I have no idea
> to improve it.
>
> Can you give me any suggestions? I am very grateful.
>
>
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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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