Hi Franz,
On Fri, 2015-11-20 at 11:07 +0100, Franz Baumdicker wrote:
> you should probably also check whether the program got into an endless
> loop? Fot larger sets of bacterial genomes I often get this problem.
> You should see always the same numbers in the output to the console in
> this case.
> Sometimes changing the order of the input genomes helps, but the more
> genomes you have the more likely you will always end in an endless loop.
This sounds like unusual behaviour. progressiveMauve does a hill
climbing optimization of the alignment anchor scores, and can
iteratively improve the anchoring many times on the same collection of
genomes, however, the loop is designed to terminate when the improvement
in score over the previous iteration is less than a particular amount.
It would be quite helpful to see the console log to understand why the
loop fails to terminate on your dataset, e.g. whether it's a bug or
something peculiar about the dataset that allows the anchoring score to
grow slowly for a very long time.
Best,
-Aaron
--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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