arzwa/beluga.jl

Statistical analysis of gene family evolution using phylogenetic birth-death processes and WGD inference using rjMCMC

beluga.jl's Issues

Invalid extinction probability, set to 1

Dear Dr Zwaenepoel

I am trying to perform WGD inference using reversible-jump MCMC using the gene count file from OrthoFinder. I am using julia-1.5.2 in a Ubuntu (18.04) remote server.
I tested with the example files 9dicots and the script worked perfectly. However, when I try to run my own data, the logpdf! output is -Inf and I end up with these warnings:

┌ Warning: Invalid extinction probability, set to 1
│ p = NaN
└ @ Beluga ~/.julia/packages/Beluga/IeAJt/src/model.jl:445
┌ Warning: Invalid extinction probability, set to 1
│ p = NaN
└ @ Beluga ~/.julia/packages/Beluga/IeAJt/src/model.jl:445
┌ Warning: Invalid extinction probability, set to 1
│ p = NaN
└ @ Beluga ~/.julia/packages/Beluga/IeAJt/src/model.jl:445
┌ Warning: Invalid extinction probability, set to 1
│ p = NaN
└ @ Beluga ~/.julia/packages/Beluga/IeAJt/src/model.jl:445
┌ Warning: Invalid extinction probability, set to 1
│ p = NaN
└ @ Beluga ~/.julia/packages/Beluga/IeAJt/src/model.jl:445
┌ Warning: Invalid extinction probability, set to 1
│ p = NaN
└ @ Beluga ~/.julia/packages/Beluga/IeAJt/src/model.jl:445
┌ Warning: Invalid extinction probability, set to 1
│ p = NaN
└ @ Beluga ~/.julia/packages/Beluga/IeAJt/src/model.jl:445

I also did the trick to enable NaN safe but this problem persists. I tried the same script a couple of months ago and I did not have this problem.

I was wondering if you know if this is a problem with my data or not.

Thank you
Cintia