Hi everyone,
I am trying to run jModelTest 2.1.7 on a group of 831 sequences. It seems to be taking a very long time to calculate the models (stuck on 0% in the completion bar and 0/88 models run for 2+ hours). I had it working with a set of approximately 370 sequences. I'm not sure if the "Likelihood scores not available" message is related to this. I tried shortening the sequence names to just the Accession numbers from GenBank, which was a fix suggested in the GitHub Forum. These are the settings I have:
Reading data file "pronghornallruminantiaprzewalskishort.fas"... OK.
number of sequences: 831
number of sites: 866
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* *
* COMPUTATION OF LIKELIHOOD SCORES WITH PHYML *
* *
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::Settings::
Phyml version = 3.0
Phyml binary = PhyML_3.0_linux64
Phyml path = /home/agrogan/nocona/jmodeltest-2.1.7/exe/phyml/
Candidate models = 88
number of substitution schemes = 11
including models with equal/unequal base frequencies (+F)
including models with/without a proportion of invariable sites (+I)
including models with/without rate variation among sites (+G) (nCat = 4)
Optimized free parameters (K) = substitution parameters + 1659 branch lengths + topology
Base tree for likelihood calculations = ML tree
Tree topology search operation = BEST
::Progress::
Model Exec. Time Total Time -lnL
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Thanks!
Angela