.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2883_91x7386_2007.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 . 526 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 4584 patterns found. (out of a total of 7386 sites) . 2512 sites without polymorphism (34.01%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1005Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 37 sec) [ -165873.8199] [Alpha ][ 0.500960] . ( 78 sec) [ -165784.5471] [24201] [depth= 3] . ( 91 sec) [ -165725.9860] [24182] [depth= 2] . ( 128 sec) [ -165702.6013] [24193] [depth= 1] . ( 142 sec) [ -165650.6875] [24194] [depth= 3] . ( 162 sec) [ -165650.6329] [24193] [depth= 1] . ( 175 sec) [ -165645.4112] [24187] [depth= 1] . ( 189 sec) [ -165558.1777] [24178] [depth= 2] . ( 202 sec) [ -165551.8125] [24178] [depth= 1] . ( 210 sec) [ -165540.7270] [24181] [depth= 1] . ( 224 sec) [ -165525.8014] [24191] [depth= 1] . ( 237 sec) [ -165523.8896] [24192] [depth= 1] . ( 250 sec) [ -165478.1477] [24191] [depth= 1] . ( 264 sec) [ -165468.2656] [24189] [depth= 1] . ( 277 sec) [ -165435.1237] [24180] [depth= 1] . ( 291 sec) [ -165377.7980] [24170] [depth= 1] . ( 312 sec) [ -163725.2314] [23722] [depth= 16] . ( 326 sec) [ -163697.2360] [23716] [depth= 1] . ( 346 sec) [ -163538.4041] [23678] [depth= 1] . ( 373 sec) [ -163460.2042] [23685] [depth= 1] . ( 386 sec) [ -163392.2867] [23678] [depth= 1] . ( 445 sec) [ -163341.5328] [23667] [depth= 1] . ( 472 sec) [ -163313.5733] [23661] [depth= 1] . ( 485 sec) [ -163264.6848] [23667] [depth= 1] . ( 513 sec) [ -163220.8074] [23659] [depth= 1] . ( 533 sec) [ -163170.0908] [23650] [depth= 1] . ( 576 sec) [ -163154.9558] [23661] [depth= 1] . ( 585 sec) [ -163128.2790] [23650] [depth= 1] . ( 598 sec) [ -163041.3216] [23666] [depth= 2] . ( 624 sec) [ -163020.6985] [23672] [depth= 1] . ( 637 sec) [ -162927.0552] [23666] [depth= 1] . ( 672 sec) [ -162811.7217] [23672] [depth= 1] . ( 710 sec) [ -162763.2576] [23664] [depth= 2] . ( 754 sec) [ -162674.4079] [23681] [depth= 1] . ( 768 sec) [ -162607.2395] [23664] [depth= 1] . ( 788 sec) [ -162597.4849] [23672] [depth= 1] . ( 802 sec) [ -162281.1251] [23673] [depth= 3] . ( 815 sec) [ -161463.8528] [23544] [depth= 3] . ( 829 sec) [ -161249.0629] [23543] [depth= 1] . ( 843 sec) [ -160994.9508] [23482] [depth= 1] . ( 857 sec) [ -160971.7286] [23480] [depth= 1] . ( 880 sec) [ -160945.8065] [23499] [depth= 1] . ( 913 sec) [ -160866.9568] [23497] [depth= 1] . ( 927 sec) [ -160828.3627] [23487] [depth= 2] . ( 940 sec) [ -160775.5617] [23485] [depth= 2] . ( 954 sec) [ -160713.7392] [23547] [depth= 1] . ( 967 sec) [ -160511.6505] [23546] [depth= 1] . ( 981 sec) [ -160476.8210] [23543] [depth= 2] . ( 996 sec) [ -160464.0430] [23539] [depth= 1] . ( 1017 sec) [ -160395.5723] [23526] [depth= 1] . ( 1058 sec) [ -160381.5762] [23517] [depth= 1] . ( 1092 sec) [ -160323.7306] [23515] [depth= 2] . ( 1119 sec) [ -160298.6795] [23497] [depth= 2] . ( 1130 sec) [ -160274.0469] [23500] [depth= 1] . ( 1143 sec) [ -160223.1510] [23494] [depth= 1] . ( 1178 sec) [ -160177.7940] [23493] [depth= 1] . ( 1195 sec) [ -160161.1957] [23483] [depth= 3] . ( 1207 sec) [ -160125.7910] [23483] [depth= 1] . ( 1248 sec) [ -160112.2345] [23483] [depth= 1] . ( 1259 sec) [ -160069.8364] [23471] [depth= 1] . ( 1301 sec) [ -160062.5162] [23476] [depth= 1] . ( 1311 sec) [ -159963.8694] [23478] [depth= 1] . ( 1418 sec) [ -159868.1345] [23463] [depth= 1] . ( 1445 sec) [ -159837.5009] [23456] [depth= 1] . ( 1482 sec) [ -159833.4866] [23460] [depth= 1] . ( 1495 sec) [ -159808.2236] [23456] [depth= 1] . ( 1526 sec) [ -159786.0524] [23449] [depth= 1] . ( 1541 sec) [ -159778.6834] [23448] [depth= 1] . ( 1588 sec) [ -159690.5153] [23446] [depth= 3] . ( 1609 sec) [ -159674.8491] [23446] [depth= 1] . ( 1622 sec) [ -159627.0259] [23446] [depth= 1] . ( 1636 sec) [ -159617.0294] [23445] [depth= 1] . ( 1666 sec) [ -159600.6205] [23450] [depth= 1] . ( 1695 sec) [ -159584.6602] [23451] [depth= 2] . ( 1714 sec) [ -159569.3339] [23460] [depth= 1] . ( 1727 sec) [ -159538.2736] [23451] [depth= 1] . ( 1742 sec) [ -159528.1431] [23448] [depth= 1] . ( 1770 sec) [ -159501.8522] [23445] [depth= 1] . ( 1785 sec) [ -159494.8746] [23445] [depth= 1] . ( 1831 sec) [ -159485.6818] [23451] [depth= 1] . ( 1870 sec) [ -157557.9265] [Branch lengths ] . ( 1894 sec) [ -157437.3640] [Alpha ][ 0.389190] . ( 2012 sec) [ -157437.3083] [23452] [depth= 1] . ( 2084 sec) [ -157432.8381] [23449] [depth= 1] . ( 2376 sec) [ -157412.0754] [23438] [depth= 1] . ( 2447 sec) [ -157337.2724] [23379] [depth= 1] . ( 2521 sec) [ -157333.7785] [23379] [depth= 1] . ( 2588 sec) [ -157330.5170] [23389] [depth= 1] . ( 2608 sec) [ -157325.9831] [23387] [depth= 1] . ( 2636 sec) [ -157316.0049] [23395] [depth= 1] . ( 2667 sec) [ -157311.4031] [23390] [depth= 1] . ( 2768 sec) [ -157309.8556] [23392] [depth= 1] . ( 2965 sec) [ -157290.9758] [23394] [depth= 4] . ( 2992 sec) [ -157279.6317] [23387] [depth= 1] . ( 3329 sec) [ -157077.7511] [Branch lengths ] . ( 3349 sec) [ -157075.6631] [Alpha ][ 0.401673] . ( 3429 sec) [ -157074.9298] [23386] [depth= 1] . ( 3999 sec) [ -157070.9212] [23390] [depth= 2] . ( 4057 sec) [ -157049.5722] [23380] [depth= 3] . ( 4757 sec) [ -157002.9350] [Branch lengths ] . ( 4777 sec) [ -157001.6889] [Alpha ][ 0.411342] . ( 6156 sec) [ -156984.0736] [Branch lengths ] . ( 6163 sec) [ -156984.0736] [Topology ] . ( 6256 sec) [ -156976.9389] [Topology ] . ( 6350 sec) [ -156970.4665] [Topology ] . ( 6444 sec) [ -156963.9595] [Topology ] . ( 6538 sec) [ -156951.0624] [Topology ] . ( 6631 sec) [ -156941.3307] [Topology ] . ( 6725 sec) [ -156940.0269] [Topology ] . ( 6819 sec) [ -156939.5319] [Topology ] . ( 6839 sec) [ -156938.6345] [Alpha ][ 0.419878] . ( 6846 sec) [ -156938.6345] [Topology ] . ( 6940 sec) [ -156938.1984] [Topology ] . ( 7034 sec) [ -156937.9121] [Topology ] . ( 7128 sec) [ -156937.7086] [Topology ] . ( 7222 sec) [ -156937.5621] [Topology ] . ( 7316 sec) [ -156937.4562] [Topology ] . ( 7410 sec) [ -156937.3794] [Topology ] . ( 7430 sec) [ -156937.3561] [Alpha ][ 0.421233] . ( 7437 sec) [ -156937.3561] [Topology ] . ( 7531 sec) [ -156937.2924] [Topology ] . ( 7625 sec) [ -156937.2466] [Topology ] . ( 7719 sec) [ -156937.2132] [Topology ] . ( 7812 sec) [ -156937.1890] [Topology ] . ( 7906 sec) [ -156937.1713] [Topology ] . ( 8000 sec) [ -156937.1584] [Topology ] . ( 8018 sec) [ -156937.1549] [Alpha ][ 0.421735] . ( 8025 sec) [ -156937.1549] [Topology ] . ( 8119 sec) [ -156937.1444] [Topology ] . ( 8213 sec) [ -156937.1368] [Topology ] . ( 8308 sec) [ -156937.1312] [Topology ] . ( 8402 sec) [ -156937.1272] [Topology ] . ( 8496 sec) [ -156937.1242] [Topology ] . ( 8590 sec) [ -156937.1220] [Topology ] . ( 8608 sec) [ -156937.1218] [Alpha ][ 0.422156] . ( 8615 sec) [ -156937.1218] [Topology ] . ( 8710 sec) [ -156937.1198] [Topology ] . ( 8804 sec) [ -156937.1183] [Topology ] . ( 8898 sec) [ -156937.1173] [Topology ] . ( 8993 sec) [ -156937.1165] [Topology ] . ( 9010 sec) [ -156937.1165] [Alpha ][ 0.422156] . ( 9018 sec) [ -156937.1165] [Topology ] . ( 9112 sec) [ -156937.1159] [Topology ] . ( 9129 sec) [ -156937.1159] [Alpha ][ 0.422156] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -156937.115938. . Printing the most likely tree in file 'proteic_M2883_91x7386_2007.phy_phyml_tree.txt'... . Time used 2h46m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 9979.88user 0.00system 2:47:04elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps