.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2771_52x1896_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 906 patterns found. (out of a total of 1896 sites) . 1193 sites without polymorphism (62.92%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -15011.6040] [GTR parameters ] . ( 2 sec) [ -14780.7799] [Alpha ][ 0.500960] . ( 3 sec) [ -14763.5982] [ 2324] [depth= 1] . ( 3 sec) [ -14761.9657] [ 2324] [depth= 1] . ( 3 sec) [ -14761.4417] [ 2324] [depth= 1] . ( 3 sec) [ -14758.9385] [ 2324] [depth= 1] . ( 5 sec) [ -14754.4887] [ 2324] [depth= 1] . ( 5 sec) [ -14748.4513] [ 2324] [depth= 1] . ( 6 sec) [ -14743.0099] [ 2319] [depth= 1] . ( 6 sec) [ -14738.9024] [ 2319] [depth= 2] . ( 6 sec) [ -14737.3266] [ 2315] [depth= 2] . ( 6 sec) [ -14736.9643] [ 2319] [depth= 1] . ( 7 sec) [ -14734.0989] [ 2314] [depth= 6] . ( 7 sec) [ -14730.1554] [ 2313] [depth= 1] . ( 8 sec) [ -14722.9291] [ 2314] [depth= 1] . ( 8 sec) [ -14717.9713] [ 2313] [depth= 1] . ( 8 sec) [ -14702.6863] [ 2315] [depth= 2] . ( 8 sec) [ -14691.6107] [ 2320] [depth= 2] . ( 9 sec) [ -14682.9433] [ 2313] [depth= 2] . ( 9 sec) [ -14679.2288] [ 2313] [depth= 1] . ( 9 sec) [ -14678.5680] [ 2313] [depth= 1] . ( 9 sec) [ -14674.6817] [ 2314] [depth= 1] . ( 9 sec) [ -14674.5900] [ 2315] [depth= 1] . ( 10 sec) [ -14671.5829] [ 2319] [depth= 3] . ( 10 sec) [ -14667.0224] [ 2319] [depth= 1] . ( 10 sec) [ -14665.6882] [ 2319] [depth= 3] . ( 11 sec) [ -14665.1291] [ 2322] [depth= 2] . ( 11 sec) [ -14664.1347] [ 2322] [depth= 2] . ( 11 sec) [ -14662.7555] [ 2321] [depth= 1] . ( 12 sec) [ -14607.8072] [Branch lengths ] . ( 18 sec) [ -14137.4679] [GTR parameters ] . ( 18 sec) [ -14024.1646] [Alpha ][ 0.250961] . ( 19 sec) [ -14023.7667] [ 2320] [depth= 1] . ( 21 sec) [ -14023.1880] [ 2320] [depth= 1] . ( 21 sec) [ -14022.2510] [ 2317] [depth= 1] . ( 23 sec) [ -14020.0959] [ 2318] [depth= 1] . ( 23 sec) [ -14011.7795] [ 2311] [depth= 4] . ( 24 sec) [ -14011.7029] [ 2317] [depth= 2] . ( 24 sec) [ -14009.5397] [ 2316] [depth= 5] . ( 25 sec) [ -14007.7856] [ 2319] [depth= 1] . ( 25 sec) [ -14007.1925] [ 2320] [depth= 2] . ( 26 sec) [ -14006.9754] [ 2319] [depth= 3] . ( 27 sec) [ -14006.2862] [ 2320] [depth= 1] . ( 27 sec) [ -14006.1857] [ 2316] [depth= 1] . ( 28 sec) [ -13993.9791] [Branch lengths ] . ( 31 sec) [ -13992.2752] [GTR parameters ] . ( 32 sec) [ -13992.1304] [Alpha ][ 0.245090] . ( 34 sec) [ -13991.7744] [ 2316] [depth= 2] . ( 35 sec) [ -13991.2847] [ 2315] [depth= 1] . ( 37 sec) [ -13989.4328] [ 2313] [depth= 2] . ( 40 sec) [ -13988.3647] [ 2317] [depth= 1] . ( 41 sec) [ -13984.6551] [Branch lengths ] . ( 41 sec) [ -13984.6546] [GTR parameters ] . ( 42 sec) [ -13984.6272] [Alpha ][ 0.247661] . ( 51 sec) [ -13984.4132] [Branch lengths ] . ( 129 sec) [ -13984.3917] [Branch lengths ] . ( 129 sec) [ -13984.3917] [Topology ] . ( 131 sec) [ -13984.3900] [Topology ] . ( 133 sec) [ -13984.3894] [Topology ] . ( 138 sec) [ -13984.3671] [GTR parameters ] . ( 138 sec) [ -13984.3627] [Alpha ][ 0.248672] . ( 138 sec) [ -13984.3627] [Topology ] . ( 140 sec) [ -13984.3612] [Topology ] . ( 142 sec) [ -13984.3606] [Topology ] . ( 145 sec) [ -13984.3605] [GTR parameters ] . ( 145 sec) [ -13984.3605] [Alpha ][ 0.248672] . ( 145 sec) [ -13984.3605] [Topology ] . ( 147 sec) [ -13984.3602] [Topology ] . ( 148 sec) [ -13984.3602] [GTR parameters ] . ( 148 sec) [ -13984.3602] [Alpha ][ 0.248672] . Checking for NNIs, optimizing five branches... . ( 163 sec) [ -13984.1458] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13984.145837. . Printing the most likely tree in file 'nucleic_M2771_52x1896_2006.phy_phyml_tree.txt'... . Time used 0h3m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 174.41user 0.00system 3:08.62elapsed 92%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps