Question: CodeML 4.9e "strange: f[132] = -0.889877 very small" messages
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gravatar for Hugo
24 months ago by
Hugo180
Universidade de Vigo, Ourense (Spain)
Hugo180 wrote:

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 • 418 views
ADD COMMENTlink written 24 months ago by Hugo180
1

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.

ADD REPLYlink modified 23 months ago • written 23 months ago by Kevin Blighe52k

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

ADD REPLYlink written 22 months ago by Hugo180
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