.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2786_104x1051_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 717 patterns found. (out of a total of 1051 sites) . 402 sites without polymorphism (38.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 39Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 8 sec) [ -16171.4937] [GTR parameters ] . ( 9 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 10 sec) [ -16051.9734] [ 3233] [depth= 1] . ( 10 sec) [ -16044.4728] [ 3239] [depth= 1] . ( 10 sec) [ -16041.2101] [ 3233] [depth= 1] . ( 10 sec) [ -16031.8120] [ 3236] [depth= 1] . ( 11 sec) [ -16014.6449] [ 3237] [depth= 1] . ( 12 sec) [ -16005.7624] [ 3238] [depth= 1] . ( 13 sec) [ -15990.6669] [ 3237] [depth= 2] . ( 15 sec) [ -15987.3566] [ 3243] [depth= 1] . ( 15 sec) [ -15961.9580] [ 3243] [depth= 1] . ( 15 sec) [ -15942.1086] [ 3236] [depth= 1] . ( 16 sec) [ -15939.0111] [ 3229] [depth= 1] . ( 16 sec) [ -15934.8211] [ 3230] [depth= 1] . ( 16 sec) [ -15906.9314] [ 3231] [depth= 2] . ( 16 sec) [ -15898.9723] [ 3225] [depth= 2] . ( 17 sec) [ -15877.6800] [ 3213] [depth= 1] . ( 18 sec) [ -15874.4025] [ 3213] [depth= 1] . ( 18 sec) [ -15869.3627] [ 3220] [depth= 1] . ( 18 sec) [ -15867.4066] [ 3215] [depth= 1] . ( 18 sec) [ -15866.6942] [ 3214] [depth= 1] . ( 19 sec) [ -15865.8712] [ 3215] [depth= 3] . ( 19 sec) [ -15865.8038] [ 3217] [depth= 3] . ( 19 sec) [ -15864.9449] [ 3217] [depth= 3] . ( 20 sec) [ -15859.3708] [ 3216] [depth= 3] . ( 20 sec) [ -15857.1233] [ 3215] [depth= 1] . ( 20 sec) [ -15855.9128] [ 3215] [depth= 1] . ( 21 sec) [ -15851.5320] [ 3221] [depth= 1] . ( 21 sec) [ -15847.7919] [ 3219] [depth= 1] . ( 22 sec) [ -15844.7681] [ 3218] [depth= 1] . ( 22 sec) [ -15840.6162] [ 3218] [depth= 1] . ( 23 sec) [ -15839.9326] [ 3217] [depth= 1] . ( 24 sec) [ -15830.1041] [ 3211] [depth= 1] . ( 24 sec) [ -15819.1369] [ 3204] [depth= 1] . ( 25 sec) [ -15819.0677] [ 3204] [depth= 1] . ( 25 sec) [ -15818.1631] [ 3204] [depth= 1] . ( 26 sec) [ -15817.6209] [ 3204] [depth= 1] . ( 26 sec) [ -15817.5540] [ 3204] [depth= 1] . ( 27 sec) [ -15808.6004] [ 3204] [depth= 1] . ( 27 sec) [ -15808.2605] [ 3203] [depth= 1] . ( 28 sec) [ -15807.9995] [ 3203] [depth= 1] . ( 29 sec) [ -15806.8027] [ 3204] [depth= 1] . ( 29 sec) [ -15805.6641] [ 3204] [depth= 1] . ( 29 sec) [ -15805.4499] [ 3203] [depth= 1] . ( 31 sec) [ -15802.3382] [ 3202] [depth= 1] . ( 31 sec) [ -15801.3906] [ 3202] [depth= 1] . ( 31 sec) [ -15800.6951] [ 3202] [depth= 1] . ( 31 sec) [ -15800.2897] [ 3202] [depth= 1] . ( 32 sec) [ -15800.1624] [ 3202] [depth= 1] . ( 33 sec) [ -15797.5178] [ 3201] [depth= 2] . ( 33 sec) [ -15796.8736] [ 3201] [depth= 3] . ( 33 sec) [ -15794.9954] [ 3201] [depth= 1] . ( 34 sec) [ -15793.7169] [ 3201] [depth= 1] . ( 34 sec) [ -15792.6062] [ 3200] [depth= 1] . ( 35 sec) [ -15791.5157] [ 3200] [depth= 1] . ( 35 sec) [ -15791.1901] [ 3200] [depth= 1] . ( 35 sec) [ -15790.4044] [ 3200] [depth= 1] . ( 35 sec) [ -15790.2498] [ 3200] [depth= 1] . ( 36 sec) [ -15789.9895] [ 3200] [depth= 1] . ( 37 sec) [ -15699.3766] [Branch lengths ] . ( 45 sec) [ -15688.8836] [GTR parameters ] . ( 45 sec) [ -15688.1073] [Alpha ][ 0.532027] . ( 46 sec) [ -15687.6214] [ 3201] [depth= 1] . ( 47 sec) [ -15687.0633] [ 3201] [depth= 1] . ( 47 sec) [ -15684.5702] [ 3201] [depth= 1] . ( 51 sec) [ -15684.0646] [ 3202] [depth= 2] . ( 52 sec) [ -15683.9292] [ 3199] [depth= 1] . ( 53 sec) [ -15683.7032] [ 3199] [depth= 1] . ( 70 sec) [ -15668.7278] [Branch lengths ] . ( 75 sec) [ -15668.5255] [GTR parameters ] . ( 76 sec) [ -15668.5192] [Alpha ][ 0.534940] . ( 80 sec) [ -15668.4728] [ 3197] [depth= 1] . ( 81 sec) [ -15668.3277] [ 3197] [depth= 1] . ( 96 sec) [ -15664.7258] [Branch lengths ] . ( 102 sec) [ -15664.6871] [GTR parameters ] . ( 102 sec) [ -15664.6608] [Alpha ][ 0.540913] . ( 125 sec) [ -15663.6809] [Branch lengths ] . ( 278 sec) [ -15663.2678] [Branch lengths ] . ( 278 sec) [ -15663.2678] [Topology ] . ( 281 sec) [ -15662.9382] [Topology ] . ( 285 sec) [ -15661.8034] [Topology ] . ( 289 sec) [ -15659.7771] [Topology ] . ( 292 sec) [ -15659.3496] [Topology ] . ( 296 sec) [ -15659.2837] [Topology ] . ( 299 sec) [ -15659.2588] [Topology ] . ( 303 sec) [ -15659.2357] [GTR parameters ] . ( 304 sec) [ -15659.2080] [Alpha ][ 0.546997] . ( 304 sec) [ -15659.2080] [Topology ] . ( 307 sec) [ -15659.1876] [Topology ] . ( 311 sec) [ -15659.1733] [Topology ] . ( 314 sec) [ -15659.1627] [Topology ] . ( 318 sec) [ -15659.1547] [Topology ] . ( 321 sec) [ -15659.1485] [Topology ] . ( 325 sec) [ -15659.1438] [Topology ] . ( 326 sec) [ -15659.1433] [GTR parameters ] . ( 326 sec) [ -15659.1432] [Alpha ][ 0.547544] . ( 326 sec) [ -15659.1432] [Topology ] . ( 329 sec) [ -15659.1392] [Topology ] . ( 333 sec) [ -15659.1361] [Topology ] . ( 337 sec) [ -15659.1337] [Topology ] . ( 340 sec) [ -15659.1319] [Topology ] . ( 344 sec) [ -15659.1304] [Topology ] . ( 347 sec) [ -15659.1293] [Topology ] . ( 348 sec) [ -15659.1291] [GTR parameters ] . ( 349 sec) [ -15659.1291] [Alpha ][ 0.547544] . ( 349 sec) [ -15659.1291] [Topology ] . ( 352 sec) [ -15659.1282] [Topology ] . ( 353 sec) [ -15659.1282] [GTR parameters ] . ( 353 sec) [ -15659.1282] [Alpha ][ 0.547544] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15659.128153. . Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'... . Time used 0h6m20s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 371.84user 0.00system 6:21.69elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps