/usr/local/phylogeny/phyml/bin/phyml.sm10.13catg.1306220729 -i input_files/20130703_155031/input.phy -d codon -b 0 --mechanistic_opt 11023 -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 WAG-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace . Sum=1.000003 . Scaling frequencies... . 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 WAG-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: 1372834231 . Subtree patterns aliasing: no . Version: 20100824-SM10 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 318 patterns found (out of a total of 1112 sites). . 832 sites without polymorphism (74.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7 Mo of memory space. . ( 0 sec) [ -6824.4953] [Branch lengths ] . ( 0 sec) [ -6811.9406] [Selective constraints on amino acids ][1.382830 * aa_fitness(a,b) + -1.795176 * (1-delta(a,b))] . ( 1 sec) [ -6772.5521] [GTR parameters ][rr_val: 0.054131 2.291978 1.315096 0.791060 1.043250 1.228929] . ( 2 sec) [ -6735.1884] [Nucleotide equlibrium freqs.][ACGT: 0.294968 0.268587 0.236831 0.199614] . ( 3 sec) [ -6733.0917] [Branch lengths ] . ( 3 sec) [ -6711.4859] [Selective constraints on amino acids ][0.715889 * aa_fitness(a,b) + -1.791876 * (1-delta(a,b))] . ( 3 sec) [ -6705.1386] [GTR parameters ][rr_val: 0.008341 3.376388 1.315096 0.791060 1.043250 1.228929] . ( 5 sec) [ -6704.2698] [Nucleotide equlibrium freqs.][ACGT: 0.318264 0.247209 0.229111 0.205416] . ( 5 sec) [ -6703.9047] [Branch lengths ] . ( 5 sec) [ -6703.3389] [Selective constraints on amino acids ][0.630777 * aa_fitness(a,b) + -1.733171 * (1-delta(a,b))] . ( 6 sec) [ -6703.2536] [GTR parameters ][rr_val: 0.004940 3.518256 1.315096 0.791060 1.043250 1.228929] . ( 7 sec) [ -6703.2435] [Nucleotide equlibrium freqs.][ACGT: 0.319362 0.245694 0.227389 0.207554] . ( 7 sec) [ -6703.2047] [Branch lengths ] . ( 7 sec) [ -6703.1166] [Selective constraints on amino acids ][0.649366 * aa_fitness(a,b) + -1.685270 * (1-delta(a,b))] . ( 8 sec) [ -6703.1165] [GTR parameters ][rr_val: 0.004796 3.523439 1.315096 0.791060 1.043250 1.228929] . ( 8 sec) [ -6703.1161] [Nucleotide equlibrium freqs.][ACGT: 0.319227 0.245956 0.226956 0.207861] . ( 8 sec) [ -6703.1150] [Branch lengths ] . ( 9 sec) [ -6703.0412] [Selective constraints on amino acids ][0.674199 * aa_fitness(a,b) + -1.652022 * (1-delta(a,b))] . ( 9 sec) [ -6703.0412] [GTR parameters ][rr_val: 0.004933 3.523439 1.315096 0.791060 1.043250 1.228929] . ( 9 sec) [ -6703.0411] [Nucleotide equlibrium freqs.][ACGT: 0.319210 0.246123 0.226732 0.207935] . ( 10 sec) [ -6703.0411] [Branch lengths ] . ( 10 sec) [ -6703.0031] [Selective constraints on amino acids ][0.692570 * aa_fitness(a,b) + -1.629060 * (1-delta(a,b))] . ( 10 sec) [ -6703.0030] [GTR parameters ][rr_val: 0.005065 3.530428 1.315096 0.791060 1.043250 1.228929] . ( 11 sec) [ -6703.0029] [Nucleotide equlibrium freqs.][ACGT: 0.319375 0.246144 0.226544 0.207936] . ( 11 sec) [ -6703.0029] [Branch lengths ] . ( 12 sec) [ -6702.9846] [Selective constraints on amino acids ][0.705355 * aa_fitness(a,b) + -1.613111 * (1-delta(a,b))] . ( 12 sec) [ -6702.9845] [GTR parameters ][rr_val: 0.005153 3.530428 1.315096 0.791060 1.043250 1.228929] . ( 12 sec) [ -6702.9845] [Nucleotide equlibrium freqs.][ACGT: 0.319360 0.246234 0.226450 0.207956] . ( 13 sec) [ -6702.9845] [Branch lengths ] . ( 13 sec) [ -6702.9757] [Selective constraints on amino acids ][0.714304 * aa_fitness(a,b) + -1.602165 * (1-delta(a,b))] . ( 13 sec) [ -6702.9756] [GTR parameters ][rr_val: 0.005220 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 14 sec) [ -6702.9756] [Nucleotide equlibrium freqs.][ACGT: 0.319430 0.246243 0.226386 0.207941] . ( 14 sec) [ -6702.9756] [Branch lengths ] . ( 15 sec) [ -6702.9714] [Selective constraints on amino acids ][0.720422 * aa_fitness(a,b) + -1.594535 * (1-delta(a,b))] . ( 15 sec) [ -6702.9714] [GTR parameters ][rr_val: 0.005220 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 15 sec) [ -6702.9714] [Nucleotide equlibrium freqs.][ACGT: 0.319438 0.246282 0.226317 0.207963] . ( 16 sec) [ -6702.9714] [Branch lengths ] . ( 16 sec) [ -6702.9694] [Selective constraints on amino acids ][0.724644 * aa_fitness(a,b) + -1.589288 * (1-delta(a,b))] . ( 16 sec) [ -6702.9694] [GTR parameters ][rr_val: 0.005286 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 17 sec) [ -6702.9694] [Nucleotide equlibrium freqs.][ACGT: 0.319449 0.246301 0.226283 0.207967] . ( 17 sec) [ -6702.9694] [Branch lengths ] . ( 17 sec) [ -6702.9684] [Selective constraints on amino acids ][0.727648 * aa_fitness(a,b) + -1.585699 * (1-delta(a,b))] . ( 18 sec) [ -6702.9684] [GTR parameters ][rr_val: 0.005286 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 18 sec) [ -6702.9684] [Nucleotide equlibrium freqs.][ACGT: 0.319456 0.246318 0.226258 0.207968] . ( 18 sec) [ -6702.9684] [Branch lengths ] . ( 19 sec) [ -6702.9679] [Selective constraints on amino acids ][0.729655 * aa_fitness(a,b) + -1.582586 * (1-delta(a,b))] . ( 19 sec) [ -6702.9679] [GTR parameters ][rr_val: 0.005286 3.540820 1.315096 0.791060 1.043250 1.228929] . ( 19 sec) [ -6702.9679] [Nucleotide equlibrium freqs.][ACGT: 0.319544 0.246272 0.226199 0.207984] . ( 20 sec) [ -6702.9677] [Selective constraints on amino acids ][0.731294 * aa_fitness(a,b) + -1.579473 * (1-delta(a,b))] . ( 20 sec) [ -6702.9677] [GTR parameters ][rr_val: 0.005286 3.540820 1.315096 0.791060 1.043250 1.228929] . ( 20 sec) [ -6702.9677] [Nucleotide equlibrium freqs.][ACGT: 0.319529 0.246292 0.226189 0.207989] . Log likelihood of the current tree: -6702.967674. . 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 0h0m20s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo