/usr/local/phylogeny/phyml/bin/phyml-mt-aa.sh is translated to /usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_174404/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: 1372841044 . Subtree patterns aliasing: no . Version: 20100824-SM10 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 78 patterns found (out of a total of 1112 sites). . 1049 sites without polymorphism (94.33%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 2 Mo of memory space. . ( 0 sec) [ -3771.2043] [Branch lengths ] . ( 0 sec) [ -3765.7927] [Selective constraints on amino acids ][1.218590 * aa_fitness(a,b) + -1.751521 * (1-delta(a,b))] . ( 1 sec) [ -3763.7952] [GTR parameters ][rr_val: 0.000000 1.523186 1.061429 1.000000 1.000000 1.000000] . ( 1 sec) [ -3762.6606] [Branch lengths ] . ( 1 sec) [ -3759.9868] [Selective constraints on amino acids ][1.059518 * aa_fitness(a,b) + -1.920203 * (1-delta(a,b))] . ( 1 sec) [ -3759.9578] [GTR parameters ][rr_val: 0.000000 1.603088 1.059788 1.000000 1.000000 1.000000] . ( 2 sec) [ -3759.9403] [Branch lengths ] . ( 2 sec) [ -3758.7219] [Selective constraints on amino acids ][0.958340 * aa_fitness(a,b) + -2.037239 * (1-delta(a,b))] . ( 2 sec) [ -3758.7165] [GTR parameters ][rr_val: 0.000000 1.615168 1.075717 1.000000 1.000000 1.000000] . ( 2 sec) [ -3758.7163] [Branch lengths ] . ( 3 sec) [ -3758.0861] [Selective constraints on amino acids ][0.886895 * aa_fitness(a,b) + -2.122047 * (1-delta(a,b))] . ( 3 sec) [ -3758.0829] [GTR parameters ][rr_val: 0.000000 1.620618 1.088702 1.000000 1.000000 1.000000] . ( 3 sec) [ -3758.0827] [Branch lengths ] . ( 3 sec) [ -3757.7532] [Selective constraints on amino acids ][0.836008 * aa_fitness(a,b) + -2.183290 * (1-delta(a,b))] . ( 4 sec) [ -3757.7516] [GTR parameters ][rr_val: 0.000000 1.625032 1.097969 1.000000 1.000000 1.000000] . ( 4 sec) [ -3757.7513] [Branch lengths ] . ( 4 sec) [ -3757.5775] [Selective constraints on amino acids ][0.799484 * aa_fitness(a,b) + -2.227367 * (1-delta(a,b))] . ( 5 sec) [ -3757.5766] [GTR parameters ][rr_val: 0.000000 1.629131 1.104436 1.000000 1.000000 1.000000] . ( 5 sec) [ -3757.5764] [Branch lengths ] . ( 5 sec) [ -3757.4837] [Selective constraints on amino acids ][0.773027 * aa_fitness(a,b) + -2.259103 * (1-delta(a,b))] . ( 5 sec) [ -3757.4832] [GTR parameters ][rr_val: 0.000000 1.630389 1.109270 1.000000 1.000000 1.000000] . ( 6 sec) [ -3757.4830] [Branch lengths ] . ( 6 sec) [ -3757.4331] [Selective constraints on amino acids ][0.753714 * aa_fitness(a,b) + -2.285765 * (1-delta(a,b))] . ( 6 sec) [ -3757.4327] [GTR parameters ][rr_val: 0.000000 1.630839 1.113779 1.000000 1.000000 1.000000] . ( 6 sec) [ -3757.4327] [Branch lengths ] . ( 7 sec) [ -3757.4057] [Selective constraints on amino acids ][0.739567 * aa_fitness(a,b) + -2.305903 * (1-delta(a,b))] . ( 7 sec) [ -3757.4055] [GTR parameters ][rr_val: 0.000000 1.631621 1.116459 1.000000 1.000000 1.000000] . ( 7 sec) [ -3757.4055] [Branch lengths ] . ( 7 sec) [ -3757.3908] [Selective constraints on amino acids ][0.729173 * aa_fitness(a,b) + -2.321218 * (1-delta(a,b))] . ( 7 sec) [ -3757.3907] [GTR parameters ][rr_val: 0.000000 1.632842 1.118514 1.000000 1.000000 1.000000] . ( 8 sec) [ -3757.3907] [Branch lengths ] . ( 8 sec) [ -3757.3827] [Selective constraints on amino acids ][0.721510 * aa_fitness(a,b) + -2.332996 * (1-delta(a,b))] . ( 8 sec) [ -3757.3826] [GTR parameters ][rr_val: 0.000000 1.637815 1.119325 1.000000 1.000000 1.000000] . ( 8 sec) [ -3757.3825] [Branch lengths ] . ( 9 sec) [ -3757.3781] [Selective constraints on amino acids ][0.715835 * aa_fitness(a,b) + -2.342194 * (1-delta(a,b))] . ( 9 sec) [ -3757.3781] [GTR parameters ][rr_val: 0.000000 1.637636 1.120342 1.000000 1.000000 1.000000] . ( 9 sec) [ -3757.3780] [Branch lengths ] . ( 9 sec) [ -3757.3757] [Selective constraints on amino acids ][0.711646 * aa_fitness(a,b) + -2.349442 * (1-delta(a,b))] . ( 10 sec) [ -3757.3757] [GTR parameters ][rr_val: 0.000000 1.638043 1.120456 1.000000 1.000000 1.000000] . ( 10 sec) [ -3757.3756] [Branch lengths ] . ( 10 sec) [ -3757.3744] [Selective constraints on amino acids ][0.708571 * aa_fitness(a,b) + -2.355233 * (1-delta(a,b))] . ( 10 sec) [ -3757.3744] [GTR parameters ][rr_val: 0.000000 1.638672 1.121800 1.000000 1.000000 1.000000] . ( 11 sec) [ -3757.3743] [Branch lengths ] . ( 11 sec) [ -3757.3736] [Selective constraints on amino acids ][0.706264 * aa_fitness(a,b) + -2.360018 * (1-delta(a,b))] . ( 11 sec) [ -3757.3736] [GTR parameters ][rr_val: 0.000000 1.638691 1.121655 1.000000 1.000000 1.000000] . ( 11 sec) [ -3757.3731] [Selective constraints on amino acids ][0.703590 * aa_fitness(a,b) + -2.360018 * (1-delta(a,b))] . ( 12 sec) [ -3757.3730] [GTR parameters ][rr_val: 0.000000 1.644262 1.120886 1.000000 1.000000 1.000000] . Log likelihood of the current tree: -3757.372956. . Printing the most likely tree in file 'input.phy_phyml_tree.txt'... . Printing the most likely tree in file 'input.phy_phyml_tree.txt'... . Time used 0h0m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo