.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2624_139x348_2006.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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... . 347 patterns found. (out of a total of 348 sites) . 60 sites without polymorphism (17.24%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis will use at least 120Mo of memory space... . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -13793.7531] [Alpha ][ 0.587356] . ( 12 sec) [ -13793.5943] [ 2318] [depth= 1] . ( 14 sec) [ -13793.3766] [ 2318] [depth= 1] . ( 16 sec) [ -13793.3429] [ 2318] [depth= 1] . ( 23 sec) [ -13793.1509] [ 2318] [depth= 1] . ( 25 sec) [ -13792.4523] [ 2318] [depth= 1] . ( 28 sec) [ -13792.4316] [ 2318] [depth= 1] . ( 39 sec) [ -13775.7445] [ 2318] [depth= 1] . ( 41 sec) [ -13765.9972] [ 2318] [depth= 1] . ( 48 sec) [ -13756.6095] [ 2315] [depth= 2] . ( 60 sec) [ -13750.1857] [ 2320] [depth= 2] . ( 63 sec) [ -13741.8524] [ 2316] [depth= 2] . ( 66 sec) [ -13735.3719] [ 2317] [depth= 1] . ( 69 sec) [ -13728.5145] [ 2314] [depth= 1] . ( 82 sec) [ -13708.6140] [ 2312] [depth= 4] . ( 85 sec) [ -13679.3687] [ 2301] [depth= 9] . ( 89 sec) [ -13666.6645] [ 2300] [depth= 1] . ( 91 sec) [ -13666.4094] [ 2300] [depth= 2] . ( 103 sec) [ -13656.4674] [ 2299] [depth= 1] . ( 111 sec) [ -13654.7024] [ 2299] [depth= 1] . ( 120 sec) [ -13630.3933] [ 2287] [depth= 11] . ( 122 sec) [ -13626.7390] [ 2286] [depth= 1] . ( 124 sec) [ -13605.0169] [ 2282] [depth= 7] . ( 128 sec) [ -13573.4086] [ 2275] [depth= 6] . ( 131 sec) [ -13529.7391] [ 2263] [depth= 11] . ( 133 sec) [ -13523.3377] [ 2262] [depth= 1] . ( 136 sec) [ -13517.0305] [ 2262] [depth= 2] . ( 139 sec) [ -13496.1905] [ 2256] [depth= 5] . ( 141 sec) [ -13480.9891] [ 2256] [depth= 3] . ( 144 sec) [ -13469.4927] [ 2256] [depth= 1] . ( 147 sec) [ -13377.4999] [ 2232] [depth= 11] . ( 152 sec) [ -13375.0787] [ 2232] [depth= 2] . ( 155 sec) [ -13372.4175] [ 2231] [depth= 3] . ( 163 sec) [ -13365.9350] [ 2229] [depth= 3] . ( 166 sec) [ -13363.8240] [ 2229] [depth= 3] . ( 169 sec) [ -13363.5463] [ 2229] [depth= 1] . ( 172 sec) [ -13353.1557] [ 2227] [depth= 2] . ( 178 sec) [ -13342.9043] [ 2222] [depth= 6] . ( 181 sec) [ -13297.1780] [ 2208] [depth= 14] . ( 183 sec) [ -13296.0102] [ 2207] [depth= 1] . ( 186 sec) [ -13295.7317] [ 2206] [depth= 3] . ( 190 sec) [ -13293.9628] [ 2206] [depth= 1] . ( 200 sec) [ -13290.8882] [ 2207] [depth= 1] . ( 202 sec) [ -13289.8877] [ 2205] [depth= 1] . ( 207 sec) [ -13288.2843] [ 2203] [depth= 6] . ( 210 sec) [ -13271.0831] [ 2200] [depth= 12] . ( 215 sec) [ -13270.8744] [ 2200] [depth= 1] . ( 221 sec) [ -13268.0798] [ 2200] [depth= 1] . ( 224 sec) [ -13267.9697] [ 2200] [depth= 1] . ( 226 sec) [ -13267.5555] [ 2200] [depth= 1] . ( 231 sec) [ -13264.9302] [ 2200] [depth= 1] . ( 234 sec) [ -13264.9160] [ 2201] [depth= 1] . ( 241 sec) [ -13261.3263] [ 2202] [depth= 1] . ( 244 sec) [ -13238.2392] [ 2201] [depth= 2] . ( 248 sec) [ -13236.8955] [ 2199] [depth= 2] . ( 256 sec) [ -13235.6635] [ 2200] [depth= 1] . ( 259 sec) [ -13234.1814] [ 2201] [depth= 1] . ( 262 sec) [ -13230.4591] [ 2200] [depth= 6] . ( 268 sec) [ -13202.2336] [ 2193] [depth= 8] . ( 272 sec) [ -13201.7595] [ 2194] [depth= 1] . ( 275 sec) [ -13200.7586] [ 2193] [depth= 1] . ( 282 sec) [ -13197.0251] [ 2193] [depth= 1] . ( 294 sec) [ -13181.4680] [ 2189] [depth= 6] . ( 300 sec) [ -13180.8117] [ 2188] [depth= 2] . ( 303 sec) [ -13178.9607] [ 2188] [depth= 1] . ( 307 sec) [ -13178.5168] [ 2188] [depth= 2] . ( 310 sec) [ -13171.8308] [ 2188] [depth= 1] . ( 313 sec) [ -13148.4243] [ 2185] [depth= 6] . ( 316 sec) [ -13142.6052] [ 2185] [depth= 3] . ( 325 sec) [ -13116.0466] [ 2180] [depth= 12] . ( 329 sec) [ -13112.3252] [ 2180] [depth= 5] . ( 332 sec) [ -13110.8021] [ 2180] [depth= 1] . ( 337 sec) [ -13110.4466] [ 2180] [depth= 2] . ( 341 sec) [ -13109.8959] [ 2180] [depth= 2] . ( 344 sec) [ -13106.5864] [ 2179] [depth= 3] . ( 349 sec) [ -13105.7032] [ 2179] [depth= 1] . ( 352 sec) [ -13104.8799] [ 2179] [depth= 1] . ( 353 sec) [ -13104.3557] [ 2180] [depth= 1] . ( 359 sec) [ -13103.9560] [ 2180] [depth= 2] . ( 362 sec) [ -13102.8489] [ 2180] [depth= 2] . ( 368 sec) [ -13102.3204] [ 2180] [depth= 1] . ( 375 sec) [ -13101.2769] [ 2180] [depth= 1] . ( 378 sec) [ -13096.9557] [ 2180] [depth= 1] . ( 384 sec) [ -13096.8524] [ 2180] [depth= 1] . ( 387 sec) [ -13096.6791] [ 2180] [depth= 2] . ( 396 sec) [ -13095.7401] [ 2180] [depth= 1] . ( 401 sec) [ -13095.5233] [ 2180] [depth= 2] . ( 404 sec) [ -13095.2266] [ 2180] [depth= 1] . ( 408 sec) [ -13094.4036] [ 2183] [depth= 1] . ( 410 sec) [ -13094.3396] [ 2183] [depth= 1] . ( 420 sec) [ -13093.0515] [ 2183] [depth= 1] . ( 422 sec) [ -13092.4238] [ 2183] [depth= 1] . ( 426 sec) [ -13089.4140] [ 2185] [depth= 1] . ( 446 sec) [ -13085.8924] [ 2184] [depth= 2] . ( 449 sec) [ -13084.6587] [ 2185] [depth= 1] . ( 452 sec) [ -13083.6631] [ 2184] [depth= 1] . ( 458 sec) [ -13083.4046] [ 2184] [depth= 1] . ( 461 sec) [ -13081.4828] [ 2184] [depth= 1] . ( 468 sec) [ -13080.9800] [ 2184] [depth= 1] . ( 475 sec) [ -13080.8568] [ 2184] [depth= 1] . ( 479 sec) [ -13080.0023] [ 2184] [depth= 1] . ( 482 sec) [ -13079.6340] [ 2184] [depth= 2] . ( 485 sec) [ -13076.7782] [ 2183] [depth= 1] . ( 491 sec) [ -13072.2755] [ 2183] [depth= 3] . ( 493 sec) [ -13072.1423] [ 2183] [depth= 1] . ( 495 sec) [ -13072.0854] [ 2183] [depth= 1] . ( 497 sec) [ -13071.8082] [ 2183] [depth= 1] . ( 500 sec) [ -13063.1843] [ 2183] [depth= 4] . ( 507 sec) [ -13060.2192] [ 2181] [depth= 1] . ( 513 sec) [ -13059.7115] [ 2181] [depth= 1] . ( 516 sec) [ -13057.9937] [ 2179] [depth= 3] . ( 519 sec) [ -13053.9417] [ 2179] [depth= 3] . ( 524 sec) [ -13051.5502] [ 2179] [depth= 1] . ( 527 sec) [ -13051.4838] [ 2179] [depth= 1] . ( 530 sec) [ -13050.6310] [ 2178] [depth= 1] . ( 533 sec) [ -13050.5912] [ 2177] [depth= 3] . ( 536 sec) [ -13048.5377] [ 2176] [depth= 1] . ( 539 sec) [ -13043.2508] [ 2176] [depth= 2] . ( 543 sec) [ -13042.6219] [ 2176] [depth= 2] . ( 551 sec) [ -13041.7051] [ 2176] [depth= 1] . ( 554 sec) [ -13039.1497] [ 2176] [depth= 3] . ( 556 sec) [ -13039.0573] [ 2176] [depth= 2] . ( 559 sec) [ -13037.6201] [ 2176] [depth= 1] . ( 562 sec) [ -13037.1464] [ 2175] [depth= 4] . ( 565 sec) [ -13036.1832] [ 2175] [depth= 1] . ( 571 sec) [ -13035.6373] [ 2176] [depth= 1] . ( 573 sec) [ -13035.0709] [ 2176] [depth= 1] . ( 579 sec) [ -13034.7599] [ 2176] [depth= 1] . ( 581 sec) [ -13031.5557] [ 2178] [depth= 3] . ( 584 sec) [ -13028.0578] [ 2175] [depth= 3] . ( 588 sec) [ -13027.2394] [ 2175] [depth= 2] . ( 597 sec) [ -12930.0645] [Branch lengths ] . ( 602 sec) [ -12926.3095] [Alpha ][ 0.702056] . ( 611 sec) [ -12926.2866] [ 2175] [depth= 1] . ( 631 sec) [ -12926.2757] [ 2175] [depth= 2] . ( 693 sec) [ -12925.2768] [ 2175] [depth= 1] . ( 696 sec) [ -12924.1565] [ 2175] [depth= 1] . ( 704 sec) [ -12924.1422] [ 2175] [depth= 1] . ( 738 sec) [ -12917.4708] [ 2175] [depth= 17] . ( 745 sec) [ -12917.4075] [ 2175] [depth= 4] . ( 748 sec) [ -12917.2356] [ 2176] [depth= 3] . ( 751 sec) [ -12915.7068] [ 2177] [depth= 1] . ( 772 sec) [ -12913.6024] [ 2176] [depth= 1] . ( 775 sec) [ -12913.4660] [ 2176] [depth= 1] . ( 782 sec) [ -12913.0266] [ 2176] [depth= 2] . ( 784 sec) [ -12908.4528] [ 2174] [depth= 1] . ( 816 sec) [ -12908.4181] [ 2174] [depth= 1] . ( 823 sec) [ -12908.4026] [ 2174] [depth= 1] . ( 825 sec) [ -12907.4117] [ 2173] [depth= 1] . ( 835 sec) [ -12905.0089] [ 2172] [depth= 10] . ( 846 sec) [ -12902.7885] [ 2172] [depth= 1] . ( 859 sec) [ -12892.0722] [ 2168] [depth= 16] . ( 866 sec) [ -12891.8011] [ 2168] [depth= 4] . ( 878 sec) [ -12891.7885] [ 2168] [depth= 2] . ( 885 sec) [ -12891.0521] [ 2168] [depth= 1] . ( 888 sec) [ -12890.8498] [ 2168] [depth= 2] . ( 891 sec) [ -12888.1114] [ 2167] [depth= 4] . ( 899 sec) [ -12887.9525] [ 2167] [depth= 10] . ( 903 sec) [ -12887.9420] [ 2167] [depth= 2] . ( 905 sec) [ -12887.5971] [ 2167] [depth= 3] . ( 918 sec) [ -12887.5846] [ 2167] [depth= 1] . ( 923 sec) [ -12887.4167] [ 2167] [depth= 2] . ( 926 sec) [ -12887.3612] [ 2167] [depth= 1] . ( 933 sec) [ -12887.3475] [ 2167] [depth= 2] . ( 941 sec) [ -12887.3117] [ 2167] [depth= 1] . ( 948 sec) [ -12887.2359] [ 2167] [depth= 1] . ( 954 sec) [ -12886.9309] [ 2167] [depth= 1] . ( 958 sec) [ -12886.8733] [ 2167] [depth= 1] . ( 961 sec) [ -12885.7424] [ 2167] [depth= 1] . ( 984 sec) [ -12885.5254] [ 2167] [depth= 1] . ( 987 sec) [ -12885.1269] [ 2167] [depth= 1] . ( 990 sec) [ -12882.6801] [ 2166] [depth= 2] . ( 991 sec) [ -12882.4739] [ 2166] [depth= 1] . ( 1000 sec) [ -12878.1130] [ 2166] [depth= 1] . ( 1009 sec) [ -12877.5320] [ 2166] [depth= 1] . ( 1010 sec) [ -12877.3929] [ 2166] [depth= 2] . ( 1013 sec) [ -12877.1158] [ 2166] [depth= 1] . ( 1018 sec) [ -12877.0098] [ 2166] [depth= 1] . ( 1024 sec) [ -12876.9478] [ 2166] [depth= 2] . ( 1027 sec) [ -12876.8670] [ 2166] [depth= 4] . ( 1031 sec) [ -12875.8072] [ 2167] [depth= 1] . ( 1033 sec) [ -12875.7938] [ 2167] [depth= 1] . ( 1043 sec) [ -12875.6191] [ 2167] [depth= 1] . ( 1045 sec) [ -12875.0047] [ 2167] [depth= 1] . ( 1048 sec) [ -12874.7480] [ 2167] [depth= 1] . ( 1050 sec) [ -12874.4626] [ 2167] [depth= 1] . ( 1052 sec) [ -12874.3484] [ 2167] [depth= 1] . ( 1055 sec) [ -12874.1916] [ 2167] [depth= 2] . ( 1058 sec) [ -12873.6939] [ 2167] [depth= 1] . ( 1060 sec) [ -12873.2265] [ 2167] [depth= 1] . ( 1062 sec) [ -12873.0235] [ 2167] [depth= 1] . ( 1063 sec) [ -12872.7150] [ 2167] [depth= 1] . ( 1068 sec) [ -12872.6686] [ 2167] [depth= 2] . ( 1072 sec) [ -12872.4536] [ 2167] [depth= 1] . ( 1074 sec) [ -12872.4199] [ 2167] [depth= 1] . ( 1081 sec) [ -12854.3748] [Branch lengths ] . ( 1084 sec) [ -12854.2809] [Alpha ][ 0.721497] . ( 1094 sec) [ -12854.2633] [ 2167] [depth= 1] . ( 1188 sec) [ -12854.1965] [ 2167] [depth= 3] . ( 1198 sec) [ -12853.6425] [ 2167] [depth= 2] . ( 1234 sec) [ -12853.5699] [ 2167] [depth= 1] . ( 1253 sec) [ -12853.5474] [ 2167] [depth= 1] . ( 1281 sec) [ -12853.3111] [ 2167] [depth= 2] . ( 1289 sec) [ -12853.3004] [ 2167] [depth= 2] . ( 1294 sec) [ -12853.2165] [ 2167] [depth= 2] . ( 1299 sec) [ -12853.1937] [ 2167] [depth= 2] . ( 1309 sec) [ -12853.0265] [ 2167] [depth= 2] . ( 1318 sec) [ -12852.9685] [ 2167] [depth= 2] . ( 1327 sec) [ -12852.4097] [ 2167] [depth= 1] . ( 1330 sec) [ -12852.1853] [ 2167] [depth= 1] . ( 1354 sec) [ -12852.1626] [ 2167] [depth= 2] . ( 1365 sec) [ -12852.0358] [ 2167] [depth= 1] . ( 1369 sec) [ -12852.0199] [ 2167] [depth= 1] . ( 1405 sec) [ -12852.0052] [ 2167] [depth= 1] . ( 1410 sec) [ -12851.9135] [ 2167] [depth= 2] . ( 1413 sec) [ -12851.8824] [ 2167] [depth= 2] . ( 1416 sec) [ -12851.8137] [ 2167] [depth= 1] . ( 1423 sec) [ -12851.4841] [ 2167] [depth= 1] . ( 1442 sec) [ -12851.3198] [ 2167] [depth= 1] . ( 1459 sec) [ -12851.2592] [ 2167] [depth= 1] . ( 1477 sec) [ -12847.7844] [Branch lengths ] . ( 1481 sec) [ -12847.7660] [Alpha ][ 0.730415] . ( 1488 sec) [ -12847.7559] [ 2167] [depth= 1] . ( 1711 sec) [ -12847.6749] [ 2167] [depth= 1] . ( 1860 sec) [ -12846.6058] [Branch lengths ] . ( 1863 sec) [ -12846.6042] [Alpha ][ 0.732977] . ( 2090 sec) [ -12846.5741] [ 2167] [depth= 2] . ( 2237 sec) [ -12846.1711] [Branch lengths ] . ( 2240 sec) [ -12846.1707] [Alpha ][ 0.734147] . ( 2241 sec) [ -12846.1707] [Topology ] . ( 2261 sec) [ -12845.9540] [Topology ] . ( 2280 sec) [ -12845.1654] [Topology ] . ( 2298 sec) [ -12843.4727] [Topology ] . ( 2318 sec) [ -12842.2005] [Topology ] . ( 2337 sec) [ -12841.6485] [Topology ] . ( 2355 sec) [ -12841.3653] [Topology ] . ( 2358 sec) [ -12841.3644] [Alpha ][ 0.736053] . ( 2360 sec) [ -12841.3644] [Topology ] . ( 2379 sec) [ -12841.2554] [Topology ] . ( 2398 sec) [ -12841.1901] [Topology ] . ( 2417 sec) [ -12841.1439] [Topology ] . ( 2436 sec) [ -12841.1103] [Topology ] . ( 2454 sec) [ -12841.0846] [Topology ] . ( 2473 sec) [ -12841.0641] [Topology ] . ( 2476 sec) [ -12841.0641] [Alpha ][ 0.736053] . ( 2477 sec) [ -12841.0641] [Topology ] . ( 2496 sec) [ -12841.0482] [Topology ] . ( 2515 sec) [ -12841.0359] [Topology ] . ( 2534 sec) [ -12841.0263] [Topology ] . ( 2553 sec) [ -12840.9867] [Topology ] . ( 2571 sec) [ -12840.8921] [Topology ] . ( 2591 sec) [ -12840.8715] [Topology ] . ( 2612 sec) [ -12840.8596] [Topology ] . ( 2634 sec) [ -12840.8512] [Topology ] . ( 2656 sec) [ -12840.8451] [Topology ] . ( 2682 sec) [ -12840.8405] [Alpha ][ 0.736053] . ( 2683 sec) [ -12840.8405] [Topology ] . ( 2705 sec) [ -12840.8371] [Topology ] . ( 2724 sec) [ -12840.8346] [Topology ] . ( 2743 sec) [ -12840.8328] [Topology ] . ( 2764 sec) [ -12840.8314] [Topology ] . ( 2784 sec) [ -12840.8303] [Topology ] . ( 2803 sec) [ -12840.8296] [Topology ] . ( 2806 sec) [ -12840.8296] [Alpha ][ 0.736053] . ( 2807 sec) [ -12840.8296] [Topology ] . ( 2827 sec) [ -12840.8290] [Topology ] . ( 2830 sec) [ -12840.8290] [Alpha ][ 0.736053] . Checking for NNIs, optimizing five branches... . ( 2974 sec) [ -12840.8206] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3123 sec) [ -12840.8178] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3286 sec) [ -12840.8171] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3407 sec) [ -12840.8080] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12840.808022. . Printing the most likely tree in file 'proteic_M2624_139x348_2006.phy_phyml_tree.txt'... . Time used 0h58m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2255.14user 0.00system 59:06.35elapsed 63%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps