[Mesquitelist] maximum file size for import into Mesquite

[Chang, Melanie]

Hi, thanks for the help.  The file I am referring to has about 160 taxa and genotypes for about 20,000 SNPs, which means that there are 40,000 characters and while I know something has to be done about having data from two alleles for each SNP, at this point I am still at the stage where I am just trying to see how large a file Mesquite can handle.

By "choke" I mean I get an out of memory error.  I tried the hi-mem version on your suggestion and while it attempts to open the file, it freezes after attempting to do so for a while.

Thanks, Melanie

-- 

Melanie Lee Chang, Ph.D. * MelanieC at lppi.ucsf.edu
Canine Behavioral Genetics Project
University of California, San Francisco
http://www.K9BehavioralGenetics.com/



-----Original Message-----
From: Wayne Maddison [mailto:wmaddisn at interchange.ubc.ca]
Sent: Tue 4/8/2008 4:59 PM
To: Chang, Melanie
Cc: mesquitelist at mesquiteproject.org
Subject: Re: [Mesquitelist] maximum file size for import into Mesquite
 
How big a file depends on memory available.  How many 
taxa/samples/individuals in your data file?

When you say "choke", what do you mean?  It gives an out of memory error?

Have you tried increasing memory allocated to Mesquite?  (See the 
file startingMesquiteAndMemoryAllocation.txt in Mesquite_Folder).

Wayne


At 4:22 PM -0700 8.4.2008, Chang, Melanie wrote:
>The subject line says it all.  How large a file can Mesquite handle? 
>In particular, I have a file containing data from approximately 
>20,000 SNPs and I can't figure out if my computer is choking on it 
>or the program is.  I'm sorry, I tried to check the archives and 
>could not find an answer to this question.
>
>Thank you.
>
>--
>
>Melanie Lee Chang, Ph.D. * MelanieC at lppi.ucsf.edu
>Canine Behavioral Genetics Project
>University of California, San Francisco
>http://www.K9BehavioralGenetics.com/
>
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-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

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CONFIDENTIALITY NOTICE This e-mail and any files or previous e-mail messages transmitted with it, may contain confidential information that is privileged or otherwise exempt from disclosure under applicable law. If you are not the intended addressee, nor authorized to receive for the intended addressee, you are hereby notified that you may not use, copy, disclose or distribute to anyone the information contained in or attached to this message. If you received this message in error, please immediately advise [Disclaimer at lppi.ucsf.edu] by reply email and delete this message, its attachments and any copies. Thank you.