.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2587_117x1910_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... . 1192 patterns found. (out of a total of 1910 sites) . 932 sites without polymorphism (48.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 74Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 8 sec) [ -17118.5858] [GTR parameters ] . ( 9 sec) [ -17061.9139] [Alpha ][ 0.510962] . ( 13 sec) [ -17061.8486] [ 2501] [depth= 1] . ( 15 sec) [ -17061.7345] [ 2501] [depth= 1] . ( 16 sec) [ -17056.0812] [ 2501] [depth= 1] . ( 17 sec) [ -17054.7927] [ 2502] [depth= 1] . ( 17 sec) [ -17048.6267] [ 2501] [depth= 1] . ( 18 sec) [ -17048.4999] [ 2501] [depth= 1] . ( 18 sec) [ -17012.5361] [ 2497] [depth= 2] . ( 21 sec) [ -17011.3277] [ 2496] [depth= 2] . ( 22 sec) [ -17000.7295] [ 2495] [depth= 1] . ( 23 sec) [ -16992.6828] [ 2494] [depth= 1] . ( 24 sec) [ -16990.6176] [ 2492] [depth= 1] . ( 26 sec) [ -16989.0410] [ 2495] [depth= 1] . ( 26 sec) [ -16985.3710] [ 2495] [depth= 1] . ( 27 sec) [ -16982.5000] [ 2495] [depth= 3] . ( 28 sec) [ -16978.3328] [ 2497] [depth= 1] . ( 29 sec) [ -16976.8263] [ 2496] [depth= 1] . ( 30 sec) [ -16976.2889] [ 2495] [depth= 2] . ( 30 sec) [ -16976.1252] [ 2495] [depth= 1] . ( 32 sec) [ -16975.7783] [ 2494] [depth= 3] . ( 33 sec) [ -16972.8399] [ 2494] [depth= 1] . ( 36 sec) [ -16934.9438] [ 2486] [depth= 1] . ( 36 sec) [ -16933.8866] [ 2486] [depth= 1] . ( 37 sec) [ -16933.7358] [ 2485] [depth= 1] . ( 37 sec) [ -16922.2618] [ 2483] [depth= 1] . ( 39 sec) [ -16918.1635] [ 2483] [depth= 1] . ( 39 sec) [ -16916.0762] [ 2483] [depth= 1] . ( 40 sec) [ -16888.7259] [ 2481] [depth= 2] . ( 40 sec) [ -16859.4034] [ 2474] [depth= 2] . ( 42 sec) [ -16858.4331] [ 2474] [depth= 3] . ( 43 sec) [ -16856.6580] [ 2472] [depth= 1] . ( 44 sec) [ -16844.6307] [ 2473] [depth= 5] . ( 44 sec) [ -16826.5778] [ 2471] [depth= 5] . ( 45 sec) [ -16825.4313] [ 2471] [depth= 1] . ( 47 sec) [ -16806.1746] [ 2475] [depth= 3] . ( 48 sec) [ -16765.4676] [ 2463] [depth= 3] . ( 48 sec) [ -16754.7893] [ 2463] [depth= 6] . ( 49 sec) [ -16704.5251] [ 2456] [depth= 6] . ( 50 sec) [ -16686.8648] [ 2454] [depth= 1] . ( 50 sec) [ -16684.6762] [ 2453] [depth= 3] . ( 51 sec) [ -16682.9271] [ 2452] [depth= 2] . ( 51 sec) [ -16673.9658] [ 2451] [depth= 3] . ( 52 sec) [ -16672.2226] [ 2452] [depth= 1] . ( 52 sec) [ -16672.0413] [ 2451] [depth= 1] . ( 53 sec) [ -16654.1867] [ 2451] [depth= 4] . ( 54 sec) [ -16648.7069] [ 2453] [depth= 1] . ( 55 sec) [ -16633.9024] [ 2451] [depth= 2] . ( 56 sec) [ -16632.5680] [ 2450] [depth= 6] . ( 56 sec) [ -16630.2375] [ 2449] [depth= 2] . ( 57 sec) [ -16629.7607] [ 2449] [depth= 1] . ( 58 sec) [ -16623.8599] [ 2448] [depth= 1] . ( 58 sec) [ -16603.1311] [ 2446] [depth= 2] . ( 59 sec) [ -16602.8354] [ 2446] [depth= 1] . ( 60 sec) [ -16595.0886] [ 2448] [depth= 6] . ( 61 sec) [ -16591.2237] [ 2447] [depth= 2] . ( 62 sec) [ -16589.2522] [ 2447] [depth= 1] . ( 62 sec) [ -16577.8139] [ 2443] [depth= 6] . ( 63 sec) [ -16577.1693] [ 2443] [depth= 1] . ( 64 sec) [ -16571.9484] [ 2443] [depth= 2] . ( 64 sec) [ -16570.6371] [ 2442] [depth= 1] . ( 65 sec) [ -16570.5395] [ 2441] [depth= 1] . ( 66 sec) [ -16558.3893] [ 2439] [depth= 2] . ( 67 sec) [ -16517.4842] [ 2438] [depth= 2] . ( 67 sec) [ -16515.9013] [ 2437] [depth= 2] . ( 68 sec) [ -16485.8123] [ 2433] [depth= 3] . ( 69 sec) [ -16475.1060] [ 2433] [depth= 2] . ( 70 sec) [ -16470.1104] [ 2430] [depth= 3] . ( 71 sec) [ -16464.7099] [ 2429] [depth= 1] . ( 71 sec) [ -16460.4493] [ 2430] [depth= 1] . ( 73 sec) [ -16454.3967] [ 2430] [depth= 1] . ( 75 sec) [ -16440.2065] [ 2430] [depth= 2] . ( 76 sec) [ -16419.6322] [ 2429] [depth= 1] . ( 76 sec) [ -16389.8177] [ 2421] [depth= 9] . ( 77 sec) [ -16386.2230] [ 2424] [depth= 1] . ( 77 sec) [ -16380.3885] [ 2421] [depth= 1] . ( 79 sec) [ -16378.9279] [ 2421] [depth= 1] . ( 80 sec) [ -16375.2617] [ 2416] [depth= 6] . ( 81 sec) [ -16374.7769] [ 2416] [depth= 1] . ( 82 sec) [ -16374.4306] [ 2416] [depth= 1] . ( 84 sec) [ -16373.2192] [ 2415] [depth= 1] . ( 86 sec) [ -16372.7736] [ 2415] [depth= 5] . ( 87 sec) [ -16372.4048] [ 2415] [depth= 1] . ( 89 sec) [ -16372.3663] [ 2415] [depth= 1] . ( 90 sec) [ -16372.2959] [ 2415] [depth= 1] . ( 91 sec) [ -16372.1765] [ 2415] [depth= 1] . ( 92 sec) [ -16372.1120] [ 2415] [depth= 1] . ( 92 sec) [ -16371.9835] [ 2415] [depth= 1] . ( 93 sec) [ -16371.8032] [ 2415] [depth= 7] . ( 94 sec) [ -16362.9582] [ 2414] [depth= 7] . ( 95 sec) [ -16361.9315] [ 2414] [depth= 3] . ( 98 sec) [ -16360.6841] [ 2413] [depth= 1] . ( 100 sec) [ -16360.2259] [ 2413] [depth= 1] . ( 100 sec) [ -16357.8048] [ 2413] [depth= 1] . ( 101 sec) [ -16355.0643] [ 2412] [depth= 4] . ( 103 sec) [ -16354.8720] [ 2412] [depth= 1] . ( 103 sec) [ -16354.8312] [ 2412] [depth= 1] . ( 104 sec) [ -16354.4776] [ 2412] [depth= 1] . ( 104 sec) [ -16354.0065] [ 2412] [depth= 1] . ( 105 sec) [ -16353.8478] [ 2412] [depth= 1] . ( 106 sec) [ -16353.7266] [ 2412] [depth= 1] . ( 106 sec) [ -16353.5655] [ 2412] [depth= 1] . ( 107 sec) [ -16353.3858] [ 2412] [depth= 1] . ( 108 sec) [ -16353.3593] [ 2412] [depth= 1] . ( 108 sec) [ -16352.3570] [ 2412] [depth= 1] . ( 109 sec) [ -16351.7424] [ 2412] [depth= 1] . ( 110 sec) [ -16351.6266] [ 2412] [depth= 2] . ( 111 sec) [ -16351.5665] [ 2412] [depth= 1] . ( 112 sec) [ -16351.4988] [ 2412] [depth= 1] . ( 116 sec) [ -16171.3613] [Branch lengths ] . ( 126 sec) [ -16168.9041] [GTR parameters ] . ( 127 sec) [ -16168.7594] [Alpha ][ 0.525494] . ( 135 sec) [ -16167.5321] [ 2411] [depth= 1] . ( 142 sec) [ -16167.4094] [ 2408] [depth= 1] . ( 145 sec) [ -16166.7356] [ 2411] [depth= 1] . ( 145 sec) [ -16166.4087] [ 2411] [depth= 1] . ( 153 sec) [ -16160.7047] [ 2410] [depth= 2] . ( 157 sec) [ -16160.4761] [ 2410] [depth= 3] . ( 159 sec) [ -16160.2278] [ 2410] [depth= 1] . ( 160 sec) [ -16160.1317] [ 2409] [depth= 2] . ( 165 sec) [ -16156.2659] [ 2411] [depth= 1] . ( 166 sec) [ -16153.6312] [ 2410] [depth= 1] . ( 167 sec) [ -16147.6653] [ 2408] [depth= 1] . ( 169 sec) [ -16146.8243] [ 2408] [depth= 1] . ( 169 sec) [ -16146.8014] [ 2408] [depth= 1] . ( 170 sec) [ -16144.4962] [ 2407] [depth= 2] . ( 171 sec) [ -16144.2471] [ 2407] [depth= 2] . ( 171 sec) [ -16136.9188] [ 2404] [depth= 3] . ( 172 sec) [ -16136.6446] [ 2406] [depth= 4] . ( 174 sec) [ -16136.2901] [ 2406] [depth= 2] . ( 177 sec) [ -16136.1511] [ 2406] [depth= 1] . ( 177 sec) [ -16136.1089] [ 2406] [depth= 1] . ( 181 sec) [ -16135.4683] [ 2406] [depth= 1] . ( 186 sec) [ -16135.4088] [ 2406] [depth= 1] . ( 189 sec) [ -16133.5603] [ 2406] [depth= 1] . ( 190 sec) [ -16133.3898] [ 2406] [depth= 2] . ( 194 sec) [ -16133.3746] [ 2406] [depth= 1] . ( 196 sec) [ -16133.3604] [ 2406] [depth= 1] . ( 199 sec) [ -16133.2297] [ 2406] [depth= 1] . ( 207 sec) [ -16133.1126] [ 2406] [depth= 1] . ( 207 sec) [ -16133.0719] [ 2406] [depth= 1] . ( 209 sec) [ -16132.8702] [ 2406] [depth= 1] . ( 211 sec) [ -16132.7335] [ 2406] [depth= 1] . ( 212 sec) [ -16132.6537] [ 2406] [depth= 2] . ( 213 sec) [ -16132.5903] [ 2406] [depth= 1] . ( 214 sec) [ -16132.5768] [ 2406] [depth= 2] . ( 215 sec) [ -16132.2357] [ 2406] [depth= 2] . ( 221 sec) [ -16076.9834] [Branch lengths ] . ( 229 sec) [ -16076.8964] [GTR parameters ] . ( 230 sec) [ -16073.7020] [Alpha ][ 0.463703] . ( 248 sec) [ -16068.6163] [ 2403] [depth= 1] . ( 256 sec) [ -16068.4172] [ 2403] [depth= 1] . ( 263 sec) [ -16067.5905] [ 2403] [depth= 1] . ( 270 sec) [ -16064.5059] [ 2403] [depth= 2] . ( 270 sec) [ -16063.8737] [ 2403] [depth= 1] . ( 273 sec) [ -16062.8873] [ 2403] [depth= 5] . ( 276 sec) [ -16061.9857] [ 2402] [depth= 1] . ( 277 sec) [ -16061.9563] [ 2402] [depth= 2] . ( 282 sec) [ -16061.8227] [ 2402] [depth= 2] . ( 299 sec) [ -16061.6546] [ 2402] [depth= 4] . ( 313 sec) [ -16061.5809] [ 2401] [depth= 2] . ( 316 sec) [ -16061.5623] [ 2401] [depth= 1] . ( 320 sec) [ -16061.5318] [ 2401] [depth= 1] . ( 326 sec) [ -16037.6488] [Branch lengths ] . ( 333 sec) [ -16037.5970] [GTR parameters ] . ( 334 sec) [ -16035.7574] [Alpha ][ 0.423690] . ( 421 sec) [ -16035.7442] [ 2403] [depth= 6] . ( 424 sec) [ -16035.7296] [ 2403] [depth= 1] . ( 427 sec) [ -16035.7133] [ 2403] [depth= 1] . ( 428 sec) [ -16035.6057] [ 2403] [depth= 1] . ( 429 sec) [ -16035.4802] [ 2403] [depth= 1] . ( 430 sec) [ -16035.0012] [ 2403] [depth= 1] . ( 433 sec) [ -16032.1279] [ 2403] [depth= 4] . ( 437 sec) [ -16032.0695] [ 2403] [depth= 1] . ( 438 sec) [ -16031.8800] [ 2403] [depth= 3] . ( 438 sec) [ -16031.8250] [ 2403] [depth= 1] . ( 439 sec) [ -16031.7665] [ 2403] [depth= 2] . ( 441 sec) [ -16031.7477] [ 2403] [depth= 1] . ( 442 sec) [ -16031.7355] [ 2403] [depth= 1] . ( 444 sec) [ -16031.6734] [ 2403] [depth= 1] . ( 445 sec) [ -16031.6585] [ 2403] [depth= 2] . ( 455 sec) [ -16018.1359] [Branch lengths ] . ( 463 sec) [ -16018.0947] [GTR parameters ] . ( 465 sec) [ -16016.8590] [Alpha ][ 0.394636] . ( 490 sec) [ -16016.6874] [ 2403] [depth= 1] . ( 542 sec) [ -16016.6747] [ 2403] [depth= 2] . ( 544 sec) [ -16016.6609] [ 2403] [depth= 1] . ( 549 sec) [ -16009.7245] [Branch lengths ] . ( 553 sec) [ -16009.7066] [GTR parameters ] . ( 554 sec) [ -16009.0508] [Alpha ][ 0.375187] . ( 639 sec) [ -16009.0406] [ 2403] [depth= 2] . ( 644 sec) [ -16005.2432] [Branch lengths ] . ( 648 sec) [ -16005.2362] [GTR parameters ] . ( 649 sec) [ -16004.9216] [Alpha ][ 0.362563] . ( 731 sec) [ -16004.9005] [ 2403] [depth= 2] . ( 735 sec) [ -16002.6008] [Branch lengths ] . ( 739 sec) [ -16002.5973] [GTR parameters ] . ( 741 sec) [ -16002.4431] [Alpha ][ 0.354163] . ( 828 sec) [ -16002.4085] [ 2403] [depth= 4] . ( 839 sec) [ -16002.1460] [ 2403] [depth= 2] . ( 843 sec) [ -16002.0829] [ 2403] [depth= 2] . ( 844 sec) [ -16002.0580] [ 2403] [depth= 3] . ( 851 sec) [ -15999.1182] [Branch lengths ] . ( 856 sec) [ -15999.1161] [GTR parameters ] . ( 858 sec) [ -15999.0474] [Alpha ][ 0.348471] . ( 939 sec) [ -15997.4044] [Branch lengths ] . ( 1315 sec) [ -15997.1297] [ 2404] [depth= 7] . ( 1318 sec) [ -15996.5870] [ 2404] [depth= 1] . ( 1334 sec) [ -15996.0796] [ 2404] [depth= 4] . ( 1340 sec) [ -15996.0136] [ 2404] [depth= 1] . ( 1343 sec) [ -15995.9494] [ 2404] [depth= 1] . ( 1352 sec) [ -15995.9033] [ 2405] [depth= 1] . ( 1353 sec) [ -15995.8928] [ 2405] [depth= 1] . ( 1365 sec) [ -15995.6872] [ 2405] [depth= 1] . ( 1367 sec) [ -15995.4548] [ 2405] [depth= 1] . ( 1367 sec) [ -15995.4438] [ 2405] [depth= 1] . ( 1382 sec) [ -15993.6031] [Branch lengths ] . ( 1386 sec) [ -15993.5902] [GTR parameters ] . ( 1387 sec) [ -15993.4863] [Alpha ][ 0.341631] . ( 1576 sec) [ -15993.3299] [ 2410] [depth= 2] . ( 1874 sec) [ -15992.9227] [ 2410] [depth= 1] . ( 1972 sec) [ -15989.9033] [Branch lengths ] . ( 1977 sec) [ -15989.8956] [GTR parameters ] . ( 1978 sec) [ -15989.8437] [Alpha ][ 0.336881] . ( 2503 sec) [ -15989.5990] [Branch lengths ] . ( 2503 sec) [ -15989.5990] [Topology ] . ( 2513 sec) [ -15989.5559] [Topology ] . ( 2523 sec) [ -15989.5349] [Topology ] . ( 2532 sec) [ -15989.5214] [Topology ] . ( 2541 sec) [ -15989.5122] [Topology ] . ( 2551 sec) [ -15989.5060] [Topology ] . ( 2560 sec) [ -15989.5016] [Topology ] . ( 2564 sec) [ -15989.5002] [GTR parameters ] . ( 2565 sec) [ -15989.4651] [Alpha ][ 0.333051] . ( 2565 sec) [ -15989.4651] [Topology ] . ( 2575 sec) [ -15989.4529] [Topology ] . ( 2585 sec) [ -15989.4450] [Topology ] . ( 2596 sec) [ -15989.4394] [Topology ] . ( 2607 sec) [ -15989.4356] [Topology ] . ( 2618 sec) [ -15989.4329] [Topology ] . ( 2629 sec) [ -15989.4310] [Topology ] . ( 2632 sec) [ -15989.4308] [GTR parameters ] . ( 2633 sec) [ -15989.4270] [Alpha ][ 0.331791] . ( 2633 sec) [ -15989.4270] [Topology ] . ( 2644 sec) [ -15989.4241] [Topology ] . ( 2657 sec) [ -15989.4221] [Topology ] . ( 2667 sec) [ -15989.4207] [Topology ] . ( 2678 sec) [ -15989.4197] [Topology ] . ( 2690 sec) [ -15989.4190] [Topology ] . ( 2692 sec) [ -15989.4189] [GTR parameters ] . ( 2693 sec) [ -15989.4182] [Alpha ][ 0.331245] . ( 2693 sec) [ -15989.4182] [Topology ] . ( 2705 sec) [ -15989.4173] [Topology ] . ( 2708 sec) [ -15989.4173] [GTR parameters ] . ( 2708 sec) [ -15989.4173] [Alpha ][ 0.331245] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15989.417294. . Printing the most likely tree in file 'nucleic_M2587_117x1910_2006.phy_phyml_tree.txt'... . Time used 0h46m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1650.01user 0.00system 46:30.82elapsed 59%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps