I am documenting this error here until someone (including myself) fixes this error.
Sometimes, the following error is given when the first likelihood is being calculated...
1: In mclapply(1:nsites.unique, MultiCoreLikelihoodBySite, mc.cores = n.cores.by.gene.by.site) :
scheduled cores 2 encountered errors in user code, all values of the jobs will be affected
Exploration of the error shows that it is somehow related to the input alignment, which in my case was a codon alignment. This can be resolved by deleting codons sites for which all taxa have an incomplete codon.
I am documenting this error here until someone (including myself) fixes this error.
Sometimes, the following error is given when the first likelihood is being calculated...
Exploration of the error shows that it is somehow related to the input alignment, which in my case was a codon alignment. This can be resolved by deleting codons sites for which all taxa have an incomplete codon.