/usr/local/phylogeny/phyml/bin/phyml-mt-aa.sh JTT-ML91+-4 -i input_files/20130703_185150/input.phy 
is translated to
/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_185150/input.phy -d aa -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix-11_mtREV JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace


. The scale_param_b for rate variation over sites has been specified; unreasonable values tend to be estimated for scale and w_0.





                                 ..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename:				 input.phy
                . Data type:					 aa
                . Alphabet size:				 64
                . Sequence format:				 interleaved
                . Number of data sets:				 1
                . Nb of bootstrapped data sets:			 0
                . Model name:					 /usr/local/phylogeny/phyml/dat/Wmatrix-11_mtREV JTT-ML91+mod-0
                . Proportion of invariable sites:		 0.000000
                . Number of substitution categs:		 1
                . Amino acid equilibrium frequencies:		 empirical
                . Optimise tree topology:			 no
                . Evaluted tree:				 file "BioNJ"
                . Optimise branch lengths:			 yes
                . Optimise substitution model parameters:	 yes
                . Run ID:					 none
                . Random seed:					 1372845110
                . Subtree patterns aliasing:			 no
                . Version:					 20100824-SM10

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 2282 patterns found (out of a total of 3618 sites). 

. 1338 sites without polymorphism (36.98%).

. Computing pairwise distances...
/usr/local/phylogeny/phyml/bin/phyml-mt-aa.sh: line 882: 10656 Killed                  /usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_185150/input.phy -d aa -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix-11_mtREV JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace