.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2862_54x1011_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 : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 587 patterns found. (out of a total of 1011 sites) . 443 sites without polymorphism (43.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -17550.8937] [GTR parameters ] . ( 1 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 1 sec) [ -17215.2965] [Topology ] . ( 2 sec) [ -16916.1845] [Topology ] . ( 4 sec) [ -16885.7882] [Topology ] . ( 5 sec) [ -16874.7992] [Topology ] . ( 6 sec) [ -16870.7493] [Topology ] . ( 8 sec) [ -16869.9252] [Topology ] . ( 9 sec) [ -16869.5950] [Topology ] . ( 10 sec) [ -16869.3884] [Topology ] . ( 12 sec) [ -16868.8474] [Topology ] . ( 13 sec) [ -16868.7091] [Topology ] . Checking for NNIs, optimizing five branches... . ( 26 sec) [ -16867.1125] [Topology ] . ( 30 sec) [ -16387.4659] [GTR parameters ] . ( 30 sec) [ -16321.3264] [Alpha ][ 0.313611] . ( 30 sec) [ -16321.3264] [Topology ] . ( 31 sec) [ -16296.0653] [Topology ] . ( 32 sec) [ -16291.6763] [Topology ] . ( 34 sec) [ -16289.9335] [Topology ] . ( 35 sec) [ -16289.0499] [Topology ] . ( 36 sec) [ -16288.5757] [Topology ] . ( 38 sec) [ -16288.3125] [Topology ] . ( 39 sec) [ -16288.1637] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -16267.6195] [GTR parameters ] . ( 55 sec) [ -16266.6873] [Alpha ][ 0.298004] . ( 55 sec) [ -16266.6873] [Topology ] . ( 56 sec) [ -16262.3457] [Topology ] . ( 58 sec) [ -16260.7450] [Topology ] . ( 59 sec) [ -16259.9619] [Topology ] . ( 60 sec) [ -16259.5615] [Topology ] . ( 62 sec) [ -16259.3516] [Topology ] . ( 63 sec) [ -16259.2400] [Topology ] . Checking for NNIs, optimizing five branches... . ( 79 sec) [ -16256.2006] [GTR parameters ] . ( 79 sec) [ -16256.1187] [Alpha ][ 0.293725] . ( 79 sec) [ -16256.1187] [Topology ] . ( 80 sec) [ -16255.1543] [Topology ] . ( 81 sec) [ -16254.7746] [Topology ] . ( 83 sec) [ -16254.5860] [Topology ] . ( 84 sec) [ -16254.4883] [Topology ] . ( 85 sec) [ -16254.4368] [Topology ] . ( 87 sec) [ -16254.4090] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -16253.8029] [GTR parameters ] . ( 101 sec) [ -16253.7748] [Alpha ][ 0.291349] . ( 101 sec) [ -16253.7748] [Topology ] . ( 102 sec) [ -16253.5624] [Topology ] . ( 104 sec) [ -16253.4790] [Topology ] . ( 105 sec) [ -16253.4367] [Topology ] . ( 106 sec) [ -16253.4143] [Topology ] . ( 108 sec) [ -16253.4022] [Topology ] . ( 109 sec) [ -16253.3957] [Topology ] . Checking for NNIs, optimizing five branches... . ( 125 sec) [ -16253.2584] [GTR parameters ] . ( 125 sec) [ -16253.2484] [Alpha ][ 0.289732] . ( 125 sec) [ -16253.2484] [Topology ] . ( 126 sec) [ -16253.1980] [Topology ] . ( 127 sec) [ -16253.1787] [Topology ] . ( 129 sec) [ -16253.1688] [Topology ] . ( 130 sec) [ -16253.1635] [Topology ] . ( 131 sec) [ -16253.1607] [Topology ] . ( 133 sec) [ -16253.1591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 147 sec) [ -16253.1248] [GTR parameters ] . ( 147 sec) [ -16253.1232] [Alpha ][ 0.289024] . ( 147 sec) [ -16253.1232] [Topology ] . ( 148 sec) [ -16253.1111] [Topology ] . ( 150 sec) [ -16253.1063] [Topology ] . ( 151 sec) [ -16253.1038] [Topology ] . ( 152 sec) [ -16253.1025] [Topology ] . ( 154 sec) [ -16253.1018] [Topology ] . Checking for NNIs, optimizing five branches... . ( 166 sec) [ -16253.0943] [GTR parameters ] . ( 166 sec) [ -16253.0940] [Alpha ][ 0.288675] . ( 166 sec) [ -16253.0940] [Topology ] . ( 168 sec) [ -16253.0908] [Topology ] . ( 169 sec) [ -16253.0895] [Topology ] . ( 171 sec) [ -16253.0888] [Topology ] . Checking for NNIs, optimizing five branches... . ( 184 sec) [ -16253.0869] [GTR parameters ] . ( 184 sec) [ -16253.0869] [Alpha ][ 0.288675] . ( 184 sec) [ -16253.0869] [Topology ] . ( 186 sec) [ -16253.0856] [Topology ] . ( 187 sec) [ -16253.0850] [Topology ] . Checking for NNIs, optimizing five branches... . ( 200 sec) [ -16253.0850] [GTR parameters ] . ( 200 sec) [ -16253.0850] [Alpha ][ 0.288675] . ( 200 sec) [ -16253.0850] [Topology ] . ( 201 sec) [ -16253.0846] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 226 sec) [ -17550.8937] [GTR parameters ] . ( 226 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 226 sec) [ -17215.2819] [ 3954] [depth= 1] . ( 227 sec) [ -17212.5717] [ 3953] [depth= 1] . ( 227 sec) [ -17211.0309] [ 3956] [depth= 1] . ( 227 sec) [ -17210.9694] [ 3957] [depth= 1] . ( 227 sec) [ -17209.0242] [ 3961] [depth= 2] . ( 227 sec) [ -17208.2432] [ 3961] [depth= 2] . ( 227 sec) [ -17196.5597] [ 3953] [depth= 1] . ( 228 sec) [ -17188.0683] [ 3957] [depth= 1] . ( 228 sec) [ -17187.7368] [ 3956] [depth= 3] . ( 228 sec) [ -17183.4824] [ 3957] [depth= 3] . ( 229 sec) [ -17182.6056] [ 3957] [depth= 1] . ( 229 sec) [ -17182.2647] [ 3957] [depth= 1] . ( 229 sec) [ -17182.0751] [ 3957] [depth= 1] . ( 229 sec) [ -17179.9553] [ 3956] [depth= 2] . ( 230 sec) [ -17171.8169] [ 3955] [depth= 2] . ( 230 sec) [ -17170.6583] [ 3954] [depth= 1] . ( 230 sec) [ -17170.3929] [ 3954] [depth= 1] . ( 230 sec) [ -17170.2910] [ 3954] [depth= 1] . ( 230 sec) [ -17170.1443] [ 3954] [depth= 1] . ( 231 sec) [ -17168.6264] [ 3957] [depth= 1] . ( 231 sec) [ -17161.6293] [ 3955] [depth= 1] . ( 231 sec) [ -17161.6041] [ 3955] [depth= 1] . ( 231 sec) [ -17159.9143] [ 3957] [depth= 1] . ( 231 sec) [ -17140.6645] [ 3974] [depth= 2] . ( 232 sec) [ -17103.7654] [ 3959] [depth= 2] . ( 232 sec) [ -17095.7780] [ 3972] [depth= 1] . ( 232 sec) [ -17081.8023] [ 3959] [depth= 1] . ( 232 sec) [ -17079.8526] [ 3952] [depth= 1] . ( 232 sec) [ -17070.9245] [ 3951] [depth= 1] . ( 232 sec) [ -17069.8324] [ 3952] [depth= 1] . ( 233 sec) [ -17066.5519] [ 3957] [depth= 1] . ( 233 sec) [ -17063.8078] [ 3954] [depth= 2] . ( 233 sec) [ -17055.2804] [ 3952] [depth= 2] . ( 233 sec) [ -17046.1616] [ 3956] [depth= 1] . ( 233 sec) [ -17044.4079] [ 3955] [depth= 1] . ( 233 sec) [ -17025.4110] [ 3953] [depth= 1] . ( 233 sec) [ -17015.1784] [ 3953] [depth= 1] . ( 233 sec) [ -16989.7343] [ 3948] [depth= 1] . ( 233 sec) [ -16988.5808] [ 3946] [depth= 1] . ( 234 sec) [ -16988.4308] [ 3948] [depth= 1] . ( 234 sec) [ -16985.2922] [ 3952] [depth= 1] . ( 234 sec) [ -16977.0947] [ 3954] [depth= 2] . ( 235 sec) [ -16913.0865] [Branch lengths ] . ( 238 sec) [ -16443.4134] [GTR parameters ] . ( 238 sec) [ -16372.1845] [Alpha ][ 0.306024] . ( 239 sec) [ -16371.6719] [ 3954] [depth= 1] . ( 239 sec) [ -16371.6338] [ 3956] [depth= 1] . ( 239 sec) [ -16371.3508] [ 3956] [depth= 2] . ( 239 sec) [ -16370.9277] [ 3959] [depth= 1] . ( 240 sec) [ -16370.5992] [ 3954] [depth= 1] . ( 240 sec) [ -16369.5120] [ 3948] [depth= 1] . ( 241 sec) [ -16369.4212] [ 3949] [depth= 1] . ( 241 sec) [ -16369.3971] [ 3949] [depth= 1] . ( 242 sec) [ -16369.3846] [ 3949] [depth= 1] . ( 242 sec) [ -16369.3197] [ 3949] [depth= 1] . ( 243 sec) [ -16361.3214] [ 3944] [depth= 1] . ( 244 sec) [ -16360.7520] [ 3947] [depth= 1] . ( 245 sec) [ -16358.8862] [ 3949] [depth= 1] . ( 245 sec) [ -16358.8613] [ 3955] [depth= 3] . ( 246 sec) [ -16346.7839] [ 3943] [depth= 2] . ( 246 sec) [ -16334.5016] [ 3944] [depth= 1] . ( 247 sec) [ -16300.4734] [Branch lengths ] . ( 251 sec) [ -16281.9168] [GTR parameters ] . ( 251 sec) [ -16281.2715] [Alpha ][ 0.292982] . ( 251 sec) [ -16280.6311] [ 3945] [depth= 1] . ( 260 sec) [ -16268.6402] [Branch lengths ] . ( 263 sec) [ -16266.1326] [GTR parameters ] . ( 263 sec) [ -16266.1321] [Alpha ][ 0.292554] . ( 272 sec) [ -16259.8282] [Branch lengths ] . ( 315 sec) [ -16258.3282] [Branch lengths ] . ( 315 sec) [ -16258.3282] [Topology ] . ( 316 sec) [ -16257.0357] [Topology ] . ( 318 sec) [ -16256.8731] [Topology ] . ( 319 sec) [ -16256.8272] [Topology ] . ( 320 sec) [ -16256.8093] [Topology ] . ( 322 sec) [ -16256.8012] [Topology ] . ( 323 sec) [ -16256.7973] [Topology ] . ( 324 sec) [ -16256.7954] [Topology ] . ( 328 sec) [ -16254.4858] [GTR parameters ] . ( 328 sec) [ -16254.4846] [Alpha ][ 0.291936] . ( 328 sec) [ -16254.4846] [Topology ] . ( 329 sec) [ -16253.9978] [Topology ] . ( 330 sec) [ -16253.8230] [Topology ] . ( 332 sec) [ -16253.7375] [Topology ] . ( 333 sec) [ -16253.6934] [Topology ] . ( 334 sec) [ -16253.6700] [Topology ] . ( 336 sec) [ -16253.6576] [Topology ] . ( 339 sec) [ -16253.4004] [GTR parameters ] . ( 340 sec) [ -16253.3884] [Alpha ][ 0.290462] . ( 340 sec) [ -16253.3884] [Topology ] . ( 341 sec) [ -16253.2950] [Topology ] . ( 342 sec) [ -16253.2583] [Topology ] . ( 344 sec) [ -16253.2394] [Topology ] . ( 345 sec) [ -16253.2294] [Topology ] . ( 346 sec) [ -16253.2240] [Topology ] . ( 348 sec) [ -16253.2211] [Topology ] . ( 351 sec) [ -16253.1616] [GTR parameters ] . ( 351 sec) [ -16253.1566] [Alpha ][ 0.289296] . ( 351 sec) [ -16253.1566] [Topology ] . ( 352 sec) [ -16253.1348] [Topology ] . ( 354 sec) [ -16253.1265] [Topology ] . ( 355 sec) [ -16253.1222] [Topology ] . ( 356 sec) [ -16253.1199] [Topology ] . ( 358 sec) [ -16253.1186] [Topology ] . ( 359 sec) [ -16253.1179] [Topology ] . ( 362 sec) [ -16253.1019] [GTR parameters ] . ( 362 sec) [ -16253.1013] [Alpha ][ 0.288818] . ( 362 sec) [ -16253.1013] [Topology ] . ( 364 sec) [ -16253.0958] [Topology ] . ( 365 sec) [ -16253.0937] [Topology ] . ( 366 sec) [ -16253.0926] [Topology ] . ( 368 sec) [ -16253.0920] [Topology ] . ( 368 sec) [ -16253.0887] [GTR parameters ] . ( 368 sec) [ -16253.0887] [Alpha ][ 0.288530] . ( 368 sec) [ -16253.0887] [Topology ] . ( 370 sec) [ -16253.0870] [Topology ] . ( 371 sec) [ -16253.0862] [Topology ] . ( 372 sec) [ -16253.0855] [GTR parameters ] . ( 372 sec) [ -16253.0855] [Alpha ][ 0.288530] . ( 372 sec) [ -16253.0855] [Topology ] . ( 373 sec) [ -16253.0846] [Topology ] . ( 374 sec) [ -16253.0845] [GTR parameters ] . ( 374 sec) [ -16253.0845] [Alpha ][ 0.288530] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -16253.084612 . Log likelihood obtained after SPR moves : -16253.084546 . Log likelihood of the current tree: -16253.084546. . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Time used 0h6m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 386.15user 0.00system 6:27.41elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps