MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000095MEGA[All Projects] Feedbackpublic2016-03-16 06:392016-03-16 12:05
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformOSOS Version
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
First NameJohn
Last NameCrooker
Emailcrooker@ucmo.edu
Confirm Emailcrooker@ucmo.edu
Summary0000095: Optimizing system performance
DescriptionI have a student that is needing to increase the speed of the program. We estimate with a standard desktop, it will take another 30 days. I have downloaded the MEGA software onto an Amazon Web Services machine with 160 GB of memory. However, the system doesn't seem to be taking advantage of the extra memory and computational speed. Do you find this to be the case that the algorithms in MEGA will not utilize the machines memory when available?
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Issue History
Date ModifiedUsernameFieldChange
2016-03-16 06:39guestNew Issue
2016-03-16 11:24gstecherAssigned To => gstecher
2016-03-16 11:24gstecherStatusnew => assigned
2016-03-16 11:24gstecherNote Deleted: 0000010
2016-03-16 11:24gstecherNote Added: 0003636
2016-03-16 11:24gstecherFile Deleted: phylip1_alignment5.txt
2016-03-16 12:05gstecherNote Added: 0003637
2016-03-16 12:05gstecherStatusassigned => resolved
2016-03-16 12:05gstecherResolutionopen => no change required

Notes
(0003636)
gstecher   
2016-03-16 11:24   
Hi John,

I am writing in response to your question regarding the MEGA software. Can you describe what it is your student is doing? Which version of MEGA is being used? Which analyses, settings, etc...? What are the characteristics of the data being used?

--
Best regards,

Glen Stecher
(0003637)
gstecher   
2016-03-16 12:05   
Hi Skip,

Thanks for the info. The student is using the ClustalW algorithm which is much slower than the other option in MEGA which is the MUSCLE algorithm. I would ask the student to use the MUSCLE algorithm and set MaxIters to 2 in the options dialog. If that is still too slow, the student can check out MAFFT (http://mafft.cbrc.jp/alignment/software/ [^]).

On 03/16/2016 11:33 AM, Skip Crooker wrote:
> Hi Glen,
>
> We are using MEGA 7.0.14(7160202-x86_64). We have sequences in a .mas file. We are aligning the sequences. Attached is an image listing the resource usage on a computer with 160GB of RAM. I'm a computer person and not familiar with the goal of the analysis. I can ask the student and her Faculty advisor to provide more insights on the exact application.
>
> In terms of the system performance, you can see the software is only using about 2% of the available memory and 3% of the computational processor speed. We estimate with just a standard desktop the alignment will take 40 days. So, I'm trying to find a way to speed this up with this more powerful computer system.
>
> Skip