Re: [Mauve-users] Crap. It's broke.

[Aaron D. <aar...@ut...>]

Hi Zachary, Mark, et al,
Glad you are able to see some humor in these error messages!
Zachary, thanks for sending the log file. From that it looks like you
are attempting an alignment of genomes that are 1.1Gbp and 597Mbp,
respectively. It also appears that your computer has about 32GB of RAM,
which unfortunately is not enough to build the sorted seed index
datastructures in memory. So progressiveMauve is trying instead to
build the index on disk, and there appears to be a bug in that very
infrequently used functionality.
If possible, I suggest getting a machine with a bit more RAM to do your
genome alignment. As a rough guess 64GB may be enough, but I can't say
with certainty. If that's not readily available in your department it's
also possible to rent machines with large memory in the Amazon EC2
cloud, for a price of course.
Best,
-Aaron
On Mon, 2016-10-03 at 17:11 +0000, Rose Mark USRE wrote:
> Don’t have an answer but, damn, I respect the candidness of that
> error!
>  
> From: ZACHARY COHEN [mailto:zc...@wi...] 
> Sent: Sunday, October 02, 2016 11:12 PM
> To: mau...@li...
> Subject: [Mauve-users] Crap. It's broke.
>  
> hello, 
> 
> I am trying to use Mauve to align my scaffolds.fa output from a
> Spades de novo assembly against a reference, but received an error.
> I've attached the error output file for your consideration and would
> greatly appreciate any feedback. Thanks again and I hope to hear from
> you soon.
> 
>  
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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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