[Primeusers] PrimeGSR memory usage

[Filipe Garrett]

The smaller dataset worked fine but I had to scale the tree root to 1.0 and use the Uniform 
distribution for the edge rates. Otherwise, I had to increase the "-c" option too much and it would 
take too long...

What do you mean by "try something immediate the two problem sizes"?

best regards,
FG


Lars Arvestad wrote:
> The alignment does not play in here. The -c option decides how many 
> discretization points you put in the species tree, and these points are 
> where gene duplications in the reconciliation are allowed to be placed. 
> With large gene trees, there is a larger need for discretization points 
> in the species tree. Also, if there are edges in the species tree that 
> are short, then you have to ask for more discretization points in order 
> to get enough points "placed" on the short species edges. This latter 
> issue is something we have a student working on (in addition to other 
> improvements and general speedups).
> 
> My recommendation would be to try something immediate the two problem 
> sizes you have now.
> 
> How has the smaller dataset worked out for you?
> 
>     Best,
>     Lars
> 
> 
> Filipe Garrett wrote:
>> Dear Lars,
>>
>> As I had already told you, I am working with two datasets: one with 90 and the other with 375 sequences.
>> With the smallest one I have no problem when I use a scaled tree to a root of 1.0 but, with the 
>> other, even with the scaled tree, I have to increase the "-c" option a lot.
>> While the first dataset works with a "-c 90", the second needs at least a "-c 650"! I've only tried 
>> until "-c 650" since, at these level, primeGSR already uses over 33Gb of memory and still outputs 
>> the error message:
>>
>> "
>> Error:
>>        Probability: Division with zero attempted!
>> "
>>
>>
>> Is this normal and is there a way to reduce memory usage?
>> Does the quality of the alignment has any influence in running time and memory usage? Does the 
>> alignment quality has a great influence on the birth and death rates estimates? I'm asking these 
>> because I'm working with a rather divergent gene family and the alignment is likely to have a lot of 
>> gaps (automatic alignment with no manual revision). I'm mainly interested on the birth and death 
>> rates estimates...
>>
>> thanks for your time,
>> FG
>>
>>   
> 
> _______________________________________________
> Primeusers mailing list
> Primeusers at sbc.su.se
> https://mail.sbc.su.se/mailman/listinfo/primeusers
> 

-- 
Filipe G. Vieira
Departament de Genetica
Universitat de Barcelona
Av. Diagonal, 645
08028 Barcelona
SPAIN
Phone: +34 934 035 306
Fax: +34 934 034 420
fgarret at ub.edu
http://www.ub.edu/molevol/