/usr/local/phylogeny/phyml/bin/phyml-codon.sh JTT-ML91+-4-E-F input_files/20130704_112221/input.phy 
is translated to
/usr/local/phylogeny/phyml/src/phyml -i input_files/20130704_112221/input.phy -d codon -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace


. Sum=1.000003
. Scaling frequencies...
Initial 0.000000

. 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:					 codon
                . 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_with_EI-11_JTT JTT-ML91+mod-0
                . Proportion of invariable sites:		 0.000000
                . Number of substitution categs:		 1
                . Codon 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:					 1372904541
                . Subtree patterns aliasing:			 no
                . Version:					 20100824-SM10

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 318 patterns found (out of a total of 1112 sites). 

. 832 sites without polymorphism (74.82%).
/usr/local/phylogeny/phyml/bin/phyml-codon.sh: line 759: 23433 Segmentation fault      /usr/local/phylogeny/phyml/src/phyml -i input_files/20130704_112221/input.phy -d codon -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace