.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2945_62x1271_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 . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 935 patterns found. (out of a total of 1271 sites) . 411 sites without polymorphism (32.34%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -36495.9506] [GTR parameters ] . ( 5 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 38 sec) [ -35998.6346] [ 9298] [depth= 1] . ( 63 sec) [ -35996.9518] [ 9294] [depth= 1] . ( 63 sec) [ -35993.4197] [ 9298] [depth= 1] . ( 70 sec) [ -35986.8893] [ 9332] [depth= 2] . ( 70 sec) [ -35944.7950] [ 9307] [depth= 2] . ( 71 sec) [ -35940.6934] [ 9305] [depth= 1] . ( 81 sec) [ -35940.5513] [ 9307] [depth= 1] . ( 83 sec) [ -35939.9674] [ 9311] [depth= 1] . ( 83 sec) [ -35926.6320] [ 9307] [depth= 1] . ( 83 sec) [ -35917.8711] [ 9323] [depth= 1] . ( 83 sec) [ -35890.1353] [ 9307] [depth= 1] . ( 83 sec) [ -35842.5750] [ 9312] [depth= 1] . ( 84 sec) [ -35840.6678] [ 9331] [depth= 2] . ( 84 sec) [ -35819.0177] [ 9320] [depth= 2] . ( 84 sec) [ -35806.2325] [ 9321] [depth= 1] . ( 91 sec) [ -35801.8228] [ 9314] [depth= 1] . ( 91 sec) [ -35801.4031] [ 9317] [depth= 1] . ( 91 sec) [ -35794.2650] [ 9314] [depth= 1] . ( 92 sec) [ -35789.9713] [ 9321] [depth= 2] . ( 92 sec) [ -35778.6166] [ 9318] [depth= 2] . ( 92 sec) [ -35776.7917] [ 9314] [depth= 1] . ( 92 sec) [ -35774.6594] [ 9312] [depth= 1] . ( 92 sec) [ -35774.2527] [ 9320] [depth= 2] . ( 94 sec) [ -35766.6697] [ 9313] [depth= 1] . ( 98 sec) [ -35765.6745] [ 9312] [depth= 1] . ( 98 sec) [ -35760.7809] [ 9300] [depth= 1] . ( 98 sec) [ -35737.7654] [ 9290] [depth= 1] . ( 99 sec) [ -35730.0055] [ 9302] [depth= 1] . ( 100 sec) [ -35723.8021] [ 9327] [depth= 1] . ( 100 sec) [ -35699.0058] [ 9302] [depth= 1] . ( 102 sec) [ -35682.4022] [ 9290] [depth= 1] . ( 106 sec) [ -35682.2733] [ 9293] [depth= 1] . ( 106 sec) [ -35680.2350] [ 9290] [depth= 1] . ( 107 sec) [ -35671.3265] [ 9299] [depth= 1] . ( 107 sec) [ -35639.6667] [ 9290] [depth= 1] . ( 107 sec) [ -35638.5014] [ 9306] [depth= 1] . ( 107 sec) [ -35617.2127] [ 9290] [depth= 1] . ( 107 sec) [ -35607.5358] [ 9299] [depth= 1] . ( 107 sec) [ -35573.3642] [ 9290] [depth= 1] . ( 111 sec) [ -35571.9205] [ 9312] [depth= 2] . ( 112 sec) [ -35571.2750] [ 9316] [depth= 1] . ( 115 sec) [ -35570.2264] [ 9336] [depth= 2] . ( 115 sec) [ -35563.4401] [ 9323] [depth= 1] . ( 118 sec) [ -35559.2157] [ 9324] [depth= 1] . ( 120 sec) [ -35557.6786] [ 9339] [depth= 3] . ( 120 sec) [ -35553.5724] [ 9329] [depth= 1] . ( 121 sec) [ -35549.5302] [ 9324] [depth= 6] . ( 122 sec) [ -35529.4529] [ 9322] [depth= 1] . ( 122 sec) [ -35522.2945] [ 9324] [depth= 1] . ( 122 sec) [ -35520.8904] [ 9317] [depth= 3] . ( 124 sec) [ -35520.1251] [ 9320] [depth= 2] . ( 125 sec) [ -35512.0542] [ 9319] [depth= 2] . ( 127 sec) [ -35500.1262] [ 9313] [depth= 2] . ( 127 sec) [ -35499.4724] [ 9302] [depth= 3] . ( 127 sec) [ -35489.8954] [ 9301] [depth= 1] . ( 127 sec) [ -35483.0479] [ 9312] [depth= 1] . ( 131 sec) [ -35480.1815] [ 9309] [depth= 2] . ( 131 sec) [ -35479.8067] [ 9315] [depth= 1] . ( 132 sec) [ -35479.4990] [ 9320] [depth= 1] . ( 134 sec) [ -35308.9432] [Branch lengths ] . ( 139 sec) [ -35259.0561] [GTR parameters ] . ( 139 sec) [ -35251.6133] [Alpha ][ 0.449359] . ( 198 sec) [ -35251.0293] [ 9311] [depth= 1] . ( 211 sec) [ -35248.7284] [ 9309] [depth= 1] . ( 230 sec) [ -35248.1310] [ 9315] [depth= 3] . ( 241 sec) [ -35244.5469] [ 9311] [depth= 1] . ( 276 sec) [ -35243.4799] [ 9308] [depth= 1] . ( 278 sec) [ -35241.1771] [ 9323] [depth= 2] . ( 295 sec) [ -35239.5071] [ 9325] [depth= 1] . ( 303 sec) [ -35230.7630] [ 9317] [depth= 1] . ( 323 sec) [ -35228.1683] [ 9311] [depth= 1] . ( 337 sec) [ -35225.8836] [ 9310] [depth= 2] . ( 337 sec) [ -35225.0772] [ 9311] [depth= 1] . ( 340 sec) [ -35183.6714] [Branch lengths ] . ( 343 sec) [ -35179.5844] [GTR parameters ] . ( 343 sec) [ -35179.5099] [Alpha ][ 0.454211] . ( 453 sec) [ -35179.3501] [ 9304] [depth= 1] . ( 486 sec) [ -35178.9975] [ 9311] [depth= 1] . ( 555 sec) [ -35162.5994] [Branch lengths ] . ( 559 sec) [ -35161.2465] [GTR parameters ] . ( 559 sec) [ -35161.2295] [Alpha ][ 0.456452] . ( 703 sec) [ -35159.5854] [ 9304] [depth= 1] . ( 771 sec) [ -35146.7180] [Branch lengths ] . ( 775 sec) [ -35145.5516] [GTR parameters ] . ( 775 sec) [ -35145.5101] [Alpha ][ 0.452976] . ( 839 sec) [ -35144.7581] [ 9308] [depth= 2] . ( 988 sec) [ -35129.2655] [Branch lengths ] . ( 992 sec) [ -35128.5390] [GTR parameters ] . ( 992 sec) [ -35128.4729] [Alpha ][ 0.448755] . ( 1207 sec) [ -35121.1530] [Branch lengths ] . ( 1261 sec) [ -35120.7326] [ 9307] [depth= 1] . ( 1293 sec) [ -35120.6799] [ 9312] [depth= 1] . ( 1296 sec) [ -35116.5004] [Branch lengths ] . ( 1299 sec) [ -35115.4867] [GTR parameters ] . ( 1299 sec) [ -35115.1879] [Alpha ][ 0.440189] . ( 1387 sec) [ -35112.7269] [Branch lengths ] . ( 1387 sec) [ -35112.7269] [Topology ] . ( 1390 sec) [ -35111.9981] [Topology ] . ( 1392 sec) [ -35111.6156] [Topology ] . ( 1394 sec) [ -35111.3487] [Topology ] . ( 1397 sec) [ -35111.0241] [Topology ] . ( 1399 sec) [ -35110.3444] [Topology ] . ( 1401 sec) [ -35110.0493] [Topology ] . ( 1403 sec) [ -35109.8575] [Topology ] . ( 1406 sec) [ -35109.7226] [Topology ] . ( 1408 sec) [ -35109.6255] [Topology ] . ( 1414 sec) [ -35108.4360] [GTR parameters ] . ( 1414 sec) [ -35107.9340] [Alpha ][ 0.429740] . ( 1414 sec) [ -35107.9340] [Topology ] . ( 1417 sec) [ -35107.5396] [Topology ] . ( 1419 sec) [ -35107.2958] [Topology ] . ( 1421 sec) [ -35107.1243] [Topology ] . ( 1423 sec) [ -35107.0020] [Topology ] . ( 1426 sec) [ -35106.9145] [Topology ] . ( 1428 sec) [ -35106.8520] [Topology ] . ( 1431 sec) [ -35106.6899] [GTR parameters ] . ( 1431 sec) [ -35106.5919] [Alpha ][ 0.425238] . ( 1431 sec) [ -35106.5919] [Topology ] . ( 1433 sec) [ -35106.4599] [Topology ] . ( 1436 sec) [ -35106.3738] [Topology ] . ( 1438 sec) [ -35106.3134] [Topology ] . ( 1440 sec) [ -35106.2706] [Topology ] . ( 1443 sec) [ -35106.2404] [Topology ] . ( 1445 sec) [ -35106.2189] [Topology ] . ( 1447 sec) [ -35106.1740] [GTR parameters ] . ( 1447 sec) [ -35106.1403] [Alpha ][ 0.422633] . ( 1447 sec) [ -35106.1403] [Topology ] . ( 1449 sec) [ -35106.0970] [Topology ] . ( 1452 sec) [ -35106.0688] [Topology ] . ( 1454 sec) [ -35106.0490] [Topology ] . ( 1456 sec) [ -35106.0352] [Topology ] . ( 1459 sec) [ -35106.0254] [Topology ] . ( 1461 sec) [ -35106.0185] [Topology ] . ( 1463 sec) [ -35106.0046] [GTR parameters ] . ( 1464 sec) [ -35105.9935] [Alpha ][ 0.421147] . ( 1464 sec) [ -35105.9935] [Topology ] . ( 1466 sec) [ -35105.9798] [Topology ] . ( 1468 sec) [ -35105.9708] [Topology ] . ( 1470 sec) [ -35105.9646] [Topology ] . ( 1473 sec) [ -35105.9602] [Topology ] . ( 1475 sec) [ -35105.9572] [Topology ] . ( 1477 sec) [ -35105.9550] [Topology ] . ( 1479 sec) [ -35105.9505] [GTR parameters ] . ( 1480 sec) [ -35105.9468] [Alpha ][ 0.420288] . ( 1480 sec) [ -35105.9468] [Topology ] . ( 1482 sec) [ -35105.9423] [Topology ] . ( 1484 sec) [ -35105.9395] [Topology ] . ( 1487 sec) [ -35105.9375] [Topology ] . ( 1489 sec) [ -35105.9361] [Topology ] . ( 1491 sec) [ -35105.9352] [Topology ] . ( 1493 sec) [ -35105.9342] [GTR parameters ] . ( 1493 sec) [ -35105.9332] [Alpha ][ 0.419841] . ( 1493 sec) [ -35105.9332] [Topology ] . ( 1495 sec) [ -35105.9316] [Topology ] . ( 1498 sec) [ -35105.9305] [Topology ] . ( 1500 sec) [ -35105.9298] [Topology ] . ( 1501 sec) [ -35105.9296] [GTR parameters ] . ( 1501 sec) [ -35105.9296] [Alpha ][ 0.419841] . ( 1501 sec) [ -35105.9296] [Topology ] . ( 1503 sec) [ -35105.9290] [Topology ] . ( 1504 sec) [ -35105.9290] [GTR parameters ] . ( 1504 sec) [ -35105.9290] [Alpha ][ 0.419422] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35105.928966. . Printing the most likely tree in file 'nucleic_M2945_62x1271_2006.phy_phyml_tree.txt'... . Time used 0h25m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1522.17user 0.00system 25:26.17elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps