Likelihood scores not available message at bottom of GUI

[Angela Grogan]

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
 
 
---------------------------------------------------------------
*                                                             *
*        COMPUTATION OF LIKELIHOOD SCORES WITH PHYML          *
*                                                             *
---------------------------------------------------------------
 
::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
-------------------------------------------------------------------------

Thanks!

Angela