Entering edit mode
6.3 years ago
Hugo
▴
380
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.
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:
[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.
Thank you for your response Kevin. Correctly, it runs to completion, but we are not sure about the meaning of these messages.