Hi. I'm using HYPHY to estimate the likelihood of correlation of dN/dS ratio between over 300 gene pairs.

The correlation model I used is from some paper and is like this (i is the branch on phylogenetic tree):

dN(Gene1,i)=tangent(slope) X dN/dS(Gene2,i) X dS(Gene1,i) + y intercept X dS(Gene1,i).

The estimation using three values of slope (-0.8, 0, 1.3) as the start points to optimize parameters, and it works in most of the case but for three of the gene pairs there are errors like this:

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:Tree2.Pxh.nonSynRate:=Tan(slope[-1.570795:-1.570795-1.570795])*Tree2.Pxh.synRate[0.3026844817213714:0-10000]*Tree1.Pxh.nonSynRate[9.882894377224147:0-10000]/Tree1.Pxh.synRate[4.097447933163494:0-10000]+yint[-3.753335124347359e+24:-1e+25-10000]*Tree2.Pxh.synRate[0.3026844817213714:0-10000] must be in [0,10000]. Current value = -1.1360762968397e+24.

Function call stack
1 : Optimize storing into, corrB_params, the following likelihood function:LF ;

As a new user to HYPHY, I'm not sure whether this is due to the model proposed. But I guess the constraint [0-10000] is intrinsic for HYPHY since I didn't find it in the batch script I used (see attachment), so I'm just wondering if you have any suggestions on why the parameters is out of boundary and how to fix this issue?

Thanks!
Jin

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