.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M3756_77x11234_2008.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... . 10843 patterns found. (out of a total of 11234 sites) . 1701 sites without polymorphism (15.14%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 2002Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 51 sec) [ -442377.5064] [Alpha ][ 0.612478] . ( 384 sec) [ -442373.6973] [87832] [depth= 2] . ( 413 sec) [ -442179.8929] [87813] [depth= 2] . ( 527 sec) [ -442165.4000] [87813] [depth= 3] . ( 555 sec) [ -442110.5094] [87798] [depth= 1] . ( 639 sec) [ -442089.9848] [87782] [depth= 9] . ( 668 sec) [ -441963.5625] [87696] [depth= 7] . ( 710 sec) [ -441947.6891] [87700] [depth= 1] . ( 742 sec) [ -441928.1827] [87696] [depth= 1] . ( 771 sec) [ -441896.9729] [87682] [depth= 8] . ( 800 sec) [ -441703.7335] [87628] [depth= 1] . ( 829 sec) [ -441611.9008] [87602] [depth= 10] . ( 860 sec) [ -441611.1636] [87578] [depth= 6] . ( 889 sec) [ -441432.7381] [87617] [depth= 1] . ( 918 sec) [ -441285.5957] [87578] [depth= 1] . ( 959 sec) [ -441283.7371] [87592] [depth= 1] . ( 990 sec) [ -441213.7431] [87574] [depth= 7] . ( 1019 sec) [ -440812.8003] [87459] [depth= 7] . ( 1049 sec) [ -440807.0990] [87445] [depth= 1] . ( 1093 sec) [ -440806.1495] [87448] [depth= 1] . ( 1152 sec) [ -440718.4452] [87428] [depth= 7] . ( 1269 sec) [ -440411.7999] [87288] [depth= 6] . ( 1301 sec) [ -440259.9153] [87302] [depth= 1] . ( 1447 sec) [ -440246.8499] [87360] [depth= 1] . ( 1502 sec) [ -439906.5514] [87283] [depth= 8] . ( 1531 sec) [ -439872.3309] [87268] [depth= 4] . ( 1563 sec) [ -439862.5824] [87263] [depth= 6] . ( 1592 sec) [ -439857.5479] [87264] [depth= 1] . ( 1645 sec) [ -439846.8872] [87256] [depth= 2] . ( 1718 sec) [ -439802.6082] [87242] [depth= 4] . ( 1746 sec) [ -439758.8396] [87224] [depth= 4] . ( 1815 sec) [ -439517.8868] [87173] [depth= 2] . ( 1844 sec) [ -439473.9549] [87136] [depth= 5] . ( 1888 sec) [ -439376.0534] [87128] [depth= 2] . ( 1917 sec) [ -439364.9574] [87114] [depth= 2] . ( 1972 sec) [ -439278.4084] [87095] [depth= 2] . ( 2001 sec) [ -438932.7594] [87006] [depth= 7] . ( 2030 sec) [ -438929.5989] [86996] [depth= 2] . ( 2058 sec) [ -438899.5603] [86978] [depth= 4] . ( 2087 sec) [ -438673.8361] [86908] [depth= 2] . ( 2115 sec) [ -438602.2954] [86865] [depth= 5] . ( 2192 sec) [ -438581.5871] [86847] [depth= 7] . ( 2315 sec) [ -438444.2169] [86740] [depth= 3] . ( 2351 sec) [ -438402.9707] [86736] [depth= 1] . ( 2399 sec) [ -438397.2375] [86735] [depth= 1] . ( 2441 sec) [ -438386.6856] [86750] [depth= 1] . ( 2471 sec) [ -438353.2147] [86750] [depth= 1] . ( 2500 sec) [ -438335.8997] [86731] [depth= 1] . ( 2536 sec) [ -438115.9909] [86637] [depth= 8] . ( 2565 sec) [ -438115.2967] [86631] [depth= 1] . ( 2612 sec) [ -438099.8693] [86628] [depth= 1] . ( 2676 sec) [ -437951.4142] [86628] [depth= 1] . ( 2737 sec) [ -437931.8377] [86624] [depth= 1] . ( 2771 sec) [ -437928.3415] [86627] [depth= 3] . ( 2820 sec) [ -437875.1454] [86633] [depth= 1] . ( 2863 sec) [ -437862.3479] [86632] [depth= 1] . ( 2907 sec) [ -437840.6271] [86629] [depth= 1] . ( 2938 sec) [ -437696.3293] [86631] [depth= 1] . ( 3006 sec) [ -437629.7561] [86605] [depth= 1] . ( 3055 sec) [ -437627.1815] [86603] [depth= 1] . ( 3109 sec) [ -437626.7962] [86608] [depth= 1] . ( 3158 sec) [ -437597.9303] [86605] [depth= 1] . ( 3258 sec) [ -437585.3292] [86593] [depth= 2] . ( 3305 sec) [ -437583.8155] [86590] [depth= 1] . ( 3337 sec) [ -437571.7791] [86586] [depth= 3] . ( 3371 sec) [ -437541.6422] [86586] [depth= 1] . ( 3455 sec) [ -435973.4529] [Branch lengths ] . ( 3503 sec) [ -435789.5580] [Alpha ][ 0.756642] . ( 3945 sec) [ -435782.3766] [86577] [depth= 2] . ( 4100 sec) [ -435738.9227] [86541] [depth= 8] . ( 4145 sec) [ -435713.8522] [86517] [depth= 7] . ( 4174 sec) [ -435670.4021] [86513] [depth= 3] . ( 4244 sec) [ -435585.5407] [86459] [depth= 2] . ( 4327 sec) [ -435569.5885] [86457] [depth= 1] . ( 4371 sec) [ -435555.1423] [86447] [depth= 4] . ( 4676 sec) [ -435534.0748] [86449] [depth= 2] . ( 4813 sec) [ -435525.4397] [86456] [depth= 2] . ( 4842 sec) [ -435521.6241] [86457] [depth= 1] . ( 4931 sec) [ -435514.1892] [86441] [depth= 15] . ( 5259 sec) [ -435490.8165] [86447] [depth= 1] . ( 5408 sec) [ -435489.7183] [86446] [depth= 1] . ( 5437 sec) [ -435467.2951] [86440] [depth= 1] . ( 5484 sec) [ -435460.3519] [86437] [depth= 1] . ( 5598 sec) [ -435436.0245] [86426] [depth= 1] . ( 5974 sec) [ -435435.6675] [86422] [depth= 1] . ( 6002 sec) [ -435431.3865] [86424] [depth= 1] . ( 6039 sec) [ -435415.5791] [86435] [depth= 1] . ( 6138 sec) [ -435004.4488] [Branch lengths ] . ( 6188 sec) [ -434997.2156] [Alpha ][ 0.788901] . ( 7710 sec) [ -434993.9399] [86433] [depth= 1] . ( 7751 sec) [ -434985.2449] [86437] [depth= 1] . ( 8057 sec) [ -434982.0353] [86439] [depth= 1] . ( 8741 sec) [ -434834.6084] [Branch lengths ] . ( 8784 sec) [ -434833.4826] [Alpha ][ 0.802214] . (10337 sec) [ -434828.1606] [86434] [depth= 1] . (10648 sec) [ -434827.0936] [86437] [depth= 2] . (11027 sec) [ -434822.9913] [86437] [depth= 2] . (11270 sec) [ -434776.0397] [Branch lengths ] . (11314 sec) [ -434775.8408] [Alpha ][ 0.807798] . (13293 sec) [ -434772.7148] [86442] [depth= 1] . (13796 sec) [ -434754.7543] [Branch lengths ] . (13835 sec) [ -434754.7396] [Alpha ][ 0.809272] . (14367 sec) [ -434746.5982] [86435] [depth= 2] . (15132 sec) [ -434745.8149] [86432] [depth= 2] . (16362 sec) [ -434736.5624] [Branch lengths ] . (16400 sec) [ -434736.5582] [Alpha ][ 0.810082] . (18916 sec) [ -434734.3747] [Branch lengths ] . (18931 sec) [ -434734.3747] [Topology ] . (19116 sec) [ -434727.5884] [Topology ] . (19301 sec) [ -434705.3709] [Topology ] . (19486 sec) [ -434663.3255] [Topology ] . (19671 sec) [ -434651.3465] [Topology ] . (19856 sec) [ -434649.2957] [Topology ] . (20041 sec) [ -434648.7463] [Topology ] . (20225 sec) [ -434648.5706] [Topology ] . (20263 sec) [ -434648.5664] [Alpha ][ 0.810892] . (20279 sec) [ -434648.5664] [Topology ] . (20463 sec) [ -434648.5072] [Topology ] . (20648 sec) [ -434648.4880] [Topology ] . (20832 sec) [ -434648.4827] [Topology ] . (21017 sec) [ -434648.4836] [Topology ] . (21055 sec) [ -434648.4836] [Alpha ][ 0.810892] . (21070 sec) [ -434648.4836] [Topology ] . (21255 sec) [ -434648.4872] [Topology ] . Moving backward . (21291 sec) [ -434648.4347] [Topology ] . (21475 sec) [ -434648.4334] [Topology ] . (21660 sec) [ -434648.4325] [Topology ] . (21698 sec) [ -434648.4325] [Alpha ][ 0.810892] . (21714 sec) [ -434648.4325] [Topology ] . (21898 sec) [ -434648.4320] [Topology ] . (21937 sec) [ -434648.4320] [Alpha ][ 0.810892] . Checking for NNIs, optimizing five branches... . (24213 sec) [ -434647.6907] [Topology ] . Checking for NNIs, optimizing five branches... . (26571 sec) [ -434638.6432] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -434638.643156. . Printing the most likely tree in file 'proteic_M3756_77x11234_2008.phy_phyml_tree.txt'... . Time used 8h1m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 28874.40user 0.00system 8:02:30elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps