Hello everyone, I would be grateful for any tips. We are trying to perform an MCMC analysis on nucleotide alignment using MrBayes on a cluster (MPI version 3.2.7a). With each run, we always get the same problem: average standard deviation of the split frequencies after some fluctuations gets to something about 0.3 and keeps jumping around this value until the end of the job, so no convergence of the chains is reached. The same task performed on a local PC (not a cluster) converges normally (based on the constant decrease in average standard deviation). The alignment is normal, there should be enough signal, etc. Has anybody had this before? Can you help? Thank you in advance!
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