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GARD freeze (Read 1862 times)
tlefebure
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Cornell University
GARD freeze
Dec 20th, 2006 at 2:47pm
 
Dear Sergei,

I ran GARD on 1200 alignments without any problem, except for one gene. The computation never stops, and I obtain the following error message:

Code:
Error:Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found. Set it by hand, or check your constraints for compatibility. Failed constraint:c_scale:=RS_1*PS_1+1*(1-PS_1)*PS_2+1*RS_3*(1-PS_1)*(1-PS_2)*PS_3+1*RS_3*RS_4*(1-PS_1)*(1-PS_2)*(1-PS_3) must be in [0,10000]. Current value = 10000.
Current BL Command:Optimize storing into, lf_MLES, the following likelihood function:lf ; 



Any idea?
I can send the mysterious alignment if you want.

Thank you,
-Tristan
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Sergei
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UCSD
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Re: GARD freeze
Reply #1 - Dec 20th, 2006 at 3:45pm
 
Dear Tristan,

This is an obscure condition which sometimes happens if the optimization algorithm fails to find a valid starting point (subject to parameter constraints). I'd like to see the alignment which gives the error, because this condition should not occur in GARD!

Cheers,
Sergei
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Division of Infectious Diseases
Division of Biomedical Informatics
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University of California San Diego
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