CodeML 4.9e "strange: f[132] = -0.889877 very small" messages

Dear colleagues,

we hare using CodeML 4.9e for analyzing a FASTA file containing 50 sequences and the model 8 is finishing in an unusual way. It spends hours and hours printing those "strange: f[x] = n very small." messages.

strange: f[132] =    -0.889877 very small. 
strange: f[133] =   -0.889893 very small.   
              log(fX) = -8624.941182  S = -8619.502108   -20.209692 
Calculating f(w|X), posterior probabilities of site classes.    did 134 / 134 patterns  9:39:10 
Time used: 9:39:11

I would be grateful if anyone could help us on understanding these messages.

Regards.

codeml paml phylogenetic

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written 8.8 years ago by Hugo 40

This will require a bit of debugging but I believe that this is a warning and not necessarily an error. It runs to completion, right?

Based on the code for this, the warning message is related to the following step:

calculate log{fX}, where fX is the marginal probability of data, and posterior of parameters postpara[]. S2 is the scale factor

[source: https://petrov.stanford.edu/software/src/paml3.15/src/codeml.c]

I can only imagine that the size of your FASTA data is not typical.

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written 8.8 years ago by Kevin Blighe 9.0K

Thank you for your response Kevin. Correctly, it runs to completion, but we are not sure about the meaning of these messages.

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written 8.7 years ago by Hugo 40

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