Hi Prabh,
by default, top sorts processes in descending order of CPU usage. If
progressiveMauve has exhausted all available memory, it may not be using
any CPU but instead simply waiting for data to be swapped between main
memory & disk storage, in which case it may not show up in top. If you
run something like:
ps -aux
(or ps -ef on the mac)
it should give a full process list which is a more definitive answer on
whether something is running or not, and what it may be doing.
If you see it there, and the memory usage is near or beyond the total
amount of RAM installed in your system, then it is likely that the
aligner has simply run out of memory and is unlikely to finish any time
soon. However, it might be possible to run it on a machine with more
RAM. If it has died entirely without error (on either stdout or stderr)
then we will need to investigate your dataset further.
-Aaron
On Fri, 2015-11-27 at 09:29 -0500, Prabh Basra wrote:
> Hi All,
>
>
>
> I am using progressive mauve to align 42 bacterial genomes (E. coli ),
> Mauve was running for about 8 days and then it stopped without giving
> any error. I am attaching the console output. There is no error,
> however it has been stuck at this point for a day and when I check if
> its running using “top”, its not running.
>
>
> Any suggestion about what is going on.
>
>
> Thanks
>
> Prabh Basra
> MSc Candidate, Carleton University
> basraprabhj...@gmail.com
>
>
>
>
>
>
>
>
>
>
>
>
>
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> 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
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