IMPORTANT WARNING: Alignment column 1390 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2064 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3106 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3122 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4325 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4326 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4327 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4328 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4329 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4330 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4331 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4332 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4333 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4334 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4335 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4336 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4337 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4338 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4339 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4340 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4341 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4342 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4343 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4344 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4345 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4346 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4347 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4348 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4349 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4350 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4351 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4352 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4353 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4354 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4355 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4356 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4357 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4358 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4359 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4360 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4361 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4362 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4363 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4364 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4365 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4366 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4367 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4368 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4369 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4370 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4371 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4372 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4373 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4374 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4375 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4376 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4377 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4378 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4379 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4380 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4381 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4382 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4383 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4384 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4385 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4386 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4390 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4509 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4573 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6279 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7373 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7440 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7441 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7442 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7443 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7444 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7450 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7451 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7452 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7453 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7454 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7455 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7456 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7457 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7458 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7459 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7460 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7461 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7462 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7463 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7464 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7465 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7473 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7479 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7480 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7481 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7482 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7483 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7484 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7485 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7486 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7487 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7488 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7489 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7490 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7491 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7492 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7493 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7494 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7495 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7496 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7497 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7498 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7499 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7500 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7501 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7502 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7503 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7504 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7505 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7506 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7507 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7508 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7509 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7510 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7511 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7512 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7513 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7514 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7515 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7516 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7517 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7518 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7843 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7844 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7845 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7846 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7847 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7848 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7849 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7850 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9223 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9224 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9225 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9226 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9227 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9228 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9229 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9230 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9231 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9232 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9233 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9234 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9235 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9236 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9237 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9238 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9239 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9240 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9266 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9267 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 161 columns that contain only undetermined values which will be treated as missing data. Normally these columns should be excluded from the analysis. Just in case you might need it, an alignment file with undetermined columns removed is printed to file /auto/dufayard/res/bigdatasets_raxml_nucl/nucleic_M4056_408x9563_2008.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 7664 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.845671 RAxML rapid hill-climbing mode Executing 1 inference on the original alignment using a distinct randomized MP tree All free model parameters will be estimated by RAxML GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Name: No Name Provided DataType: DNA Substitution Matrix: GTR Empirical Base Frequencies: pi(A): 0.256233 pi(C): 0.221105 pi(G): 0.262974 pi(T): 0.259688 313.741290 -187050.424613 499.012240 -186340.706095 1154.486960 -186224.406404 2484.936006 -186046.113546 4458.828861 -185810.576064 6947.848106 -185712.952584 7102.894141 -185276.200103 8711.061126 -184923.813100 9936.147690 -184808.479593 10995.426048 -184760.835060 11922.462183 -184734.699219 12798.894566 -184719.427472 13630.214529 -184708.974727 14463.497391 -184705.266456 15253.368906 -184699.925195 16042.910140 -184698.141166 16769.230173 -184697.457904 17481.253163 -184697.026749 18225.538741 -184695.270886 18969.400429 -184695.086476 19801.026404 -184694.957811 20565.407045 -184694.869449 22390.956520 -184694.443587 24069.998071 -184694.357318 25605.708959 -184693.760222 27780.522525 -184693.658972 29592.679879 -184693.576274 31193.801232 -184693.493567 34174.482600 -184687.488272 36304.278264 -184683.653506 38139.301220 -184678.809503 39638.941441 -184677.867842 41060.412157 -184677.306736 42411.140762 -184676.759198 43749.505806 -184676.679996 45024.001391 -184676.604384 47758.753607 -184676.526167 50652.921179 -184676.526167 51491.901965 -184667.983792 Overall Time for 1 Inference 51491.968973 Likelihood : -184667.983792 Parsimony starting tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_parsimonyTree.nucleic_M4056_408x9563_2008.phy_RAXML Final tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_result.nucleic_M4056_408x9563_2008.phy_RAXML Execution Log File written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_log.nucleic_M4056_408x9563_2008.phy_RAXML Execution information file written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_info.nucleic_M4056_408x9563_2008.phy_RAXML