.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2946_110x1003_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 614 patterns found. (out of a total of 1003 sites) . 462 sites without polymorphism (46.06%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -18030.1538] [GTR parameters ] . ( 7 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 7 sec) [ -17732.2284] [ 3534] [depth= 1] . ( 7 sec) [ -17725.2109] [ 3534] [depth= 2] . ( 7 sec) [ -17714.4305] [ 3532] [depth= 2] . ( 8 sec) [ -17699.4618] [ 3534] [depth= 1] . ( 8 sec) [ -17689.8725] [ 3529] [depth= 1] . ( 8 sec) [ -17688.3653] [ 3528] [depth= 1] . ( 9 sec) [ -17681.2030] [ 3522] [depth= 1] . ( 10 sec) [ -17680.9559] [ 3522] [depth= 1] . ( 10 sec) [ -17677.3635] [ 3521] [depth= 1] . ( 10 sec) [ -17676.8722] [ 3521] [depth= 1] . ( 10 sec) [ -17674.4552] [ 3521] [depth= 1] . ( 11 sec) [ -17674.2568] [ 3521] [depth= 1] . ( 11 sec) [ -17671.7383] [ 3528] [depth= 1] . ( 12 sec) [ -17658.4736] [ 3529] [depth= 1] . ( 12 sec) [ -17658.3159] [ 3528] [depth= 2] . ( 12 sec) [ -17657.1404] [ 3528] [depth= 1] . ( 12 sec) [ -17656.8457] [ 3528] [depth= 1] . ( 13 sec) [ -17652.7493] [ 3525] [depth= 1] . ( 14 sec) [ -17652.3796] [ 3523] [depth= 1] . ( 14 sec) [ -17652.0395] [ 3523] [depth= 1] . ( 14 sec) [ -17650.0752] [ 3523] [depth= 1] . ( 14 sec) [ -17624.3696] [ 3522] [depth= 3] . ( 15 sec) [ -17623.8893] [ 3522] [depth= 1] . ( 15 sec) [ -17613.5812] [ 3520] [depth= 2] . ( 15 sec) [ -17613.4797] [ 3520] [depth= 1] . ( 16 sec) [ -17612.9331] [ 3522] [depth= 1] . ( 16 sec) [ -17605.6162] [ 3525] [depth= 1] . ( 17 sec) [ -17604.7951] [ 3522] [depth= 1] . ( 17 sec) [ -17602.1778] [ 3521] [depth= 1] . ( 17 sec) [ -17594.5542] [ 3522] [depth= 1] . ( 18 sec) [ -17590.3246] [ 3525] [depth= 1] . ( 18 sec) [ -17581.9401] [ 3523] [depth= 2] . ( 18 sec) [ -17580.6208] [ 3524] [depth= 1] . ( 19 sec) [ -17575.8494] [ 3521] [depth= 3] . ( 19 sec) [ -17569.3253] [ 3515] [depth= 2] . ( 19 sec) [ -17567.3614] [ 3514] [depth= 1] . ( 19 sec) [ -17565.2150] [ 3515] [depth= 2] . ( 20 sec) [ -17564.8530] [ 3515] [depth= 1] . ( 20 sec) [ -17555.5997] [ 3513] [depth= 1] . ( 20 sec) [ -17546.6927] [ 3509] [depth= 2] . ( 20 sec) [ -17545.6543] [ 3509] [depth= 1] . ( 21 sec) [ -17540.8514] [ 3509] [depth= 2] . ( 21 sec) [ -17528.3073] [ 3505] [depth= 1] . ( 22 sec) [ -17528.2121] [ 3505] [depth= 1] . ( 22 sec) [ -17526.1176] [ 3506] [depth= 1] . ( 23 sec) [ -17521.9638] [ 3509] [depth= 1] . ( 23 sec) [ -17515.6466] [ 3509] [depth= 1] . ( 23 sec) [ -17511.9577] [ 3508] [depth= 1] . ( 24 sec) [ -17506.2224] [ 3509] [depth= 2] . ( 24 sec) [ -17504.4521] [ 3509] [depth= 1] . ( 24 sec) [ -17502.0559] [ 3511] [depth= 1] . ( 25 sec) [ -17488.0883] [ 3511] [depth= 1] . ( 25 sec) [ -17484.8274] [ 3509] [depth= 1] . ( 25 sec) [ -17484.0254] [ 3510] [depth= 1] . ( 25 sec) [ -17478.2402] [ 3509] [depth= 1] . ( 26 sec) [ -17466.8086] [ 3510] [depth= 2] . ( 26 sec) [ -17465.5204] [ 3512] [depth= 1] . ( 26 sec) [ -17464.5300] [ 3510] [depth= 1] . ( 27 sec) [ -17454.7444] [ 3506] [depth= 2] . ( 27 sec) [ -17450.2192] [ 3511] [depth= 1] . ( 27 sec) [ -17447.3360] [ 3506] [depth= 1] . ( 27 sec) [ -17402.6116] [ 3501] [depth= 9] . ( 28 sec) [ -17401.8552] [ 3502] [depth= 1] . ( 28 sec) [ -17401.0523] [ 3501] [depth= 1] . ( 28 sec) [ -17400.8666] [ 3502] [depth= 1] . ( 28 sec) [ -17399.1278] [ 3504] [depth= 7] . ( 28 sec) [ -17391.8649] [ 3504] [depth= 2] . ( 29 sec) [ -17386.7120] [ 3504] [depth= 1] . ( 29 sec) [ -17377.1882] [ 3498] [depth= 1] . ( 29 sec) [ -17372.0638] [ 3497] [depth= 1] . ( 29 sec) [ -17369.2684] [ 3503] [depth= 1] . ( 30 sec) [ -17361.5347] [ 3497] [depth= 1] . ( 30 sec) [ -17353.2333] [ 3492] [depth= 1] . ( 30 sec) [ -17351.0608] [ 3494] [depth= 1] . ( 31 sec) [ -17345.2271] [ 3494] [depth= 1] . ( 31 sec) [ -17337.2483] [ 3490] [depth= 2] . ( 31 sec) [ -17336.2752] [ 3490] [depth= 1] . ( 31 sec) [ -17333.0543] [ 3490] [depth= 1] . ( 32 sec) [ -17330.7882] [ 3490] [depth= 1] . ( 32 sec) [ -17326.2528] [ 3491] [depth= 1] . ( 32 sec) [ -17323.5188] [ 3490] [depth= 1] . ( 32 sec) [ -17320.8707] [ 3491] [depth= 1] . ( 32 sec) [ -17316.1338] [ 3490] [depth= 1] . ( 33 sec) [ -17313.6395] [ 3488] [depth= 1] . ( 33 sec) [ -17313.6208] [ 3486] [depth= 1] . ( 34 sec) [ -17309.9958] [ 3487] [depth= 1] . ( 34 sec) [ -17307.2945] [ 3486] [depth= 1] . ( 36 sec) [ -17136.6460] [Branch lengths ] . ( 41 sec) [ -17123.5531] [GTR parameters ] . ( 41 sec) [ -17085.1300] [Alpha ][ 0.346155] . ( 43 sec) [ -17083.8389] [ 3488] [depth= 1] . ( 43 sec) [ -17075.9860] [ 3482] [depth= 1] . ( 45 sec) [ -17074.0956] [ 3477] [depth= 2] . ( 45 sec) [ -17071.7742] [ 3478] [depth= 1] . ( 46 sec) [ -17071.0813] [ 3480] [depth= 1] . ( 47 sec) [ -17070.6640] [ 3479] [depth= 1] . ( 48 sec) [ -17069.1000] [ 3479] [depth= 1] . ( 51 sec) [ -17069.0192] [ 3478] [depth= 1] . ( 57 sec) [ -17068.6911] [ 3477] [depth= 1] . ( 58 sec) [ -17063.0393] [ 3477] [depth= 4] . ( 58 sec) [ -17062.8356] [ 3476] [depth= 1] . ( 60 sec) [ -17060.9918] [ 3477] [depth= 1] . ( 61 sec) [ -17030.0554] [Branch lengths ] . ( 66 sec) [ -17028.5717] [GTR parameters ] . ( 66 sec) [ -17028.4000] [Alpha ][ 0.354100] . ( 88 sec) [ -17022.1811] [Branch lengths ] . ( 122 sec) [ -17021.9139] [ 3480] [depth= 1] . ( 123 sec) [ -17021.7428] [ 3478] [depth= 1] . ( 187 sec) [ -17020.8774] [ 3484] [depth= 3] . ( 192 sec) [ -17019.9517] [ 3486] [depth= 1] . ( 194 sec) [ -17019.1706] [ 3485] [depth= 6] . ( 197 sec) [ -17009.5334] [ 3477] [depth= 1] . ( 222 sec) [ -17009.4966] [ 3480] [depth= 1] . ( 232 sec) [ -17002.4636] [Branch lengths ] . ( 236 sec) [ -17002.2438] [GTR parameters ] . ( 236 sec) [ -17002.1299] [Alpha ][ 0.360878] . ( 302 sec) [ -17002.0877] [ 3481] [depth= 1] . ( 330 sec) [ -16999.6157] [ 3480] [depth= 1] . ( 393 sec) [ -16997.7244] [Branch lengths ] . ( 398 sec) [ -16997.7142] [GTR parameters ] . ( 399 sec) [ -16997.7139] [Alpha ][ 0.361238] . ( 606 sec) [ -16997.6825] [ 3482] [depth= 5] . ( 644 sec) [ -16995.5154] [Branch lengths ] . ( 650 sec) [ -16995.5072] [GTR parameters ] . ( 650 sec) [ -16995.5068] [Alpha ][ 0.361600] . ( 859 sec) [ -16995.4289] [ 3483] [depth= 1] . ( 871 sec) [ -16994.3502] [ 3483] [depth= 1] . ( 898 sec) [ -16993.1296] [Branch lengths ] . ( 902 sec) [ -16993.1232] [GTR parameters ] . ( 902 sec) [ -16993.1220] [Alpha ][ 0.362272] . ( 1152 sec) [ -16993.0210] [Branch lengths ] . ( 1152 sec) [ -16993.0210] [Topology ] . ( 1157 sec) [ -16993.0047] [Topology ] . ( 1163 sec) [ -16992.9969] [Topology ] . ( 1169 sec) [ -16992.9918] [Topology ] . ( 1175 sec) [ -16992.9883] [Topology ] . ( 1181 sec) [ -16992.9859] [Topology ] . ( 1186 sec) [ -16992.9843] [Topology ] . ( 1191 sec) [ -16992.9801] [GTR parameters ] . ( 1192 sec) [ -16992.9788] [Alpha ][ 0.362938] . ( 1192 sec) [ -16992.9788] [Topology ] . ( 1197 sec) [ -16992.9768] [Topology ] . ( 1203 sec) [ -16992.9755] [Topology ] . ( 1208 sec) [ -16992.9745] [Topology ] . ( 1209 sec) [ -16992.9744] [GTR parameters ] . ( 1210 sec) [ -16992.9744] [Alpha ][ 0.362938] . ( 1210 sec) [ -16992.9744] [Topology ] . ( 1215 sec) [ -16992.9737] [Topology ] . ( 1216 sec) [ -16992.9737] [GTR parameters ] . ( 1217 sec) [ -16992.9737] [Alpha ][ 0.362938] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16992.973662. . Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'... . Time used 0h20m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 878.09user 0.00system 21:00.75elapsed 69%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps