Dear Sarah,

One of the nodes on our cluster seems to have developed hardware problems - thus the hung jobs. I restarted the queue just now, having taken the problem node out of the pool; we'll see how that goes.

You can indeed increase the number of categories when running the analysis locally, and also tighten the convergence criterion (e.g. not 30 generations with no c-AIC improvement, but 50 or 100).

Using a consistent tree would be a good idea, because lineage specific analyses could be influenced quite a bit by the changes in the topology. I could take a look at the specific outputs which generate different results and see if anything else stands out; it's a bit difficult to speak in generalities and be helpful here:)


Cheers,
Sergei

Dear Sarah,

Two months? Wow! Did you use the branch length approximation heuristic? It speeds things up by a factor of 50x or so, and almost always gets the same results.

Cheers,
Sergei

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