Re: [Mauve-users] Mauve time and memory requirements

[Franz B. <fra...@gm...>]

Hi Susan,

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.

I would be very interested in a solution for this, if this is your issue 
and you can find one.

Greetings from Germany,

Franz

------

Dr. Franz Baumdicker
University of Freiburg

bau...@st...


Am 19.11.2015 um 22:44 schrieb Aaron Darling:
> Hi Susan,
>
> On Thu, 2015-11-19 at 20:52 +0000, Susan Beth Fogelson wrote:
>> I am using Mauve to align approximately 35 bacterial genomes to a
>> reference.  Currently I am using a desktop computer with 16GB of RAM.
>> I started the alignment about 2 days ago and it is still running, is
>> this a normal time frame?  Is there a way I can let the program access
>> more memory to have it run more efficiently or do you suggest I use a
>> computer with more power?
>
> You should be able to determine if progressiveMauve is running out of
> memory by looking at a task/process manager. If on linux you could try
> top, on windows the task manager (via Ctrl+Alt+Esc) or on mac the
> "Activity Monitor" from the utilities folder. If you see a lot of disk
> activity, or that the progressiveMauve process is running at much less
> than 100% CPU, combined with a allocated memory footprint (VM size)
> approaching your system memory size, then it is likely the program needs
> more memory.
>
> If you don't see those symptoms then it's probably already going as fast
> as it can as currently implemented. progressiveMauve runs
> single-threaded (e.g. no multi-core CPU support) and a few days of
> compute does not sound unusual for a dataset of the size you describe.
>
> Best,
> -Aaron
>
> --
> 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.
>
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Mauve-users mailing list
> Mau...@li...
> https://lists.sourceforge.net/lists/listinfo/mauve-users
>