Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2696_50x1472_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 Starting tree : BIONJ Optimise tree topology : yes Optimise branch lengths and rate parameters : yes . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 19630472 . Log(lk) : * -> -6289.224082 . Log(lk) : -6289.224082 -> -6268.806800 6 swaps done . Log(lk) : -6268.806800 -> -6264.332544 3 swaps done . Log(lk) : -6264.332544 -> -6262.550255 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6172.212630 -> -6171.847144 3 swaps done . Log(lk) : -6171.847144 -> -6171.816160 1 swap done . Log(lk) : -6171.816160 -> -6171.747633 1 swap done . Log(lk) : -6171.747633 -> -6171.801872 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.747633 -> -6171.642900 1 swap done . Log(lk) : -6171.642900 -> -6171.604463 0 swap done . Log(lk) : -6171.604463 -> -6171.601090 0 swap done . Log(lk) : -6171.601090 -> -6171.600515 0 swap done . Last optimization step... . Log(lk) : * -> -6171.600379 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600379 -> -6171.600312 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600312 -> -6171.600309 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600309 -> -6171.600307 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600307 -> -6171.600306 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600306 -> -6171.600304 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600304 -> -6171.600303 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600303 -> -6171.600302 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600302 -> -6171.600301 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600301 -> -6171.600299 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600299 -> -6171.600298 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600298 -> -6171.600297 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600297 -> -6171.600296 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600296 -> -6171.600294 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600294 -> -6171.600293 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600293 -> -6171.600292 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600292 -> -6171.600291 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600291 -> -6171.600289 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600289 -> -6171.600288 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600288 -> -6171.600287 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600287 -> -6171.600286 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600286 -> -6171.600284 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600284 -> -6171.600283 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600283 -> -6171.600282 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600282 -> -6171.600281 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600281 -> -6171.600279 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600279 -> -6171.600278 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600278 -> -6171.600277 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600277 -> -6171.600276 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600276 -> -6171.600274 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600274 -> -6171.600273 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600273 -> -6171.600272 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600272 -> -6171.600271 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600271 -> -6171.600270 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600270 -> -6171.600268 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600268 -> -6171.600267 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600267 -> -6171.600266 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600266 -> -6171.600265 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600265 -> -6171.600263 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600263 -> -6171.600262 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600262 -> -6171.600261 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600261 -> -6171.600260 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600260 -> -6171.600258 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600258 -> -6171.600257 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600257 -> -6171.600256 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600256 -> -6171.600255 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600255 -> -6171.600254 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600254 -> -6171.600252 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600252 -> -6171.600251 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600251 -> -6171.600250 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600250 -> -6171.600249 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600249 -> -6171.600248 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600248 -> -6171.600246 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600246 -> -6171.600245 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600245 -> -6171.600244 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600244 -> -6171.600243 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600243 -> -6171.600241 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600241 -> -6171.600240 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600240 -> -6171.600239 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600239 -> -6171.600238 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600238 -> -6171.600237 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600237 -> -6171.600235 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600235 -> -6171.600234 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600234 -> -6171.600233 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600233 -> -6171.600232 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600232 -> -6171.600231 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600231 -> -6171.600229 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600229 -> -6171.600228 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600228 -> -6171.600227 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600227 -> -6171.600226 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600226 -> -6171.600225 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600225 -> -6171.600223 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600223 -> -6171.600222 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600222 -> -6171.600221 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600221 -> -6171.600220 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600220 -> -6171.600219 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600219 -> -6171.600217 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600217 -> -6171.600216 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600216 -> -6171.600215 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600215 -> -6171.600214 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600214 -> -6171.600213 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600213 -> -6171.600212 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600212 -> -6171.600210 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600210 -> -6171.600209 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600209 -> -6171.600208 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600208 -> -6171.600207 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600207 -> -6171.600206 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600206 -> -6171.600204 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600204 -> -6171.600203 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600203 -> -6171.600202 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600202 -> -6171.600201 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600201 -> -6171.600200 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600200 -> -6171.600199 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600199 -> -6171.600197 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600197 -> -6171.600196 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600196 -> -6171.600195 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600195 -> -6171.600194 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600194 -> -6171.600193 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600193 -> -6171.600191 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6171.600191 -> -6171.600190 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -6171.600190 . Time used 0h5m49s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 344.22user 0.00system 5:49.16elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps