IMPORTANT WARNING: Alignment column 589 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 590 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 591 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 800 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 939 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 940 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1390 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1431 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1432 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1524 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1525 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1526 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1527 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1528 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1529 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1530 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1531 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1532 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1533 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1534 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1535 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1536 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1537 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1538 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1539 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1586 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1587 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1588 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1589 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1590 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1591 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1592 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1593 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1594 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1595 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1596 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1789 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1800 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1801 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1885 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1886 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1887 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1888 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1889 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1899 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1900 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1901 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2240 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2275 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2276 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2277 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2317 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2318 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2319 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2320 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2321 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2322 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2323 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2324 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2325 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2326 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2327 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2868 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2869 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2870 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3050 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3105 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3313 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3314 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 Found 71 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_M4058_406x6016_2008.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 5231 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.689524 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): 0.250605 pi(C): 0.270466 pi(G): 0.251903 pi(T): 0.227026 187.478094 -473464.380107 306.517896 -473135.107466 753.177029 -472087.026989 1224.849267 -471539.477988 1631.267891 -471372.181800 2010.563845 -471203.162891 2350.232266 -471178.348427 2673.324902 -471168.213044 2988.622615 -471163.273391 3299.231385 -471160.454856 3618.842928 -471151.942813 3944.170308 -471150.363783 4658.025625 -471073.171280 5320.717456 -471066.176008 5923.550590 -471064.330687 6516.158533 -471062.651951 7096.876721 -471061.511546 7717.423370 -471040.098987 8309.722917 -471036.811850 8877.970382 -471036.522573 9449.604478 -471036.336049 10024.417986 -471036.238408 10595.181436 -470997.791772 11532.414177 -470958.427848 12275.071447 -470952.825485 12933.693423 -470952.727096 13562.047425 -470952.628557 14649.555339 -470860.986025 15708.378217 -470835.580047 16535.737419 -470832.978200 17219.338112 -470832.381299 17848.953333 -470832.286232 18521.750895 -470823.198068 19525.884856 -470819.756970 20294.272555 -470818.959669 21020.326814 -470817.185480 21662.695177 -470816.984898 22234.174661 -470816.889618 23314.029736 -470816.795620 24431.712492 -470721.014914 25415.976692 -470704.183708 26173.417162 -470694.643761 26814.322485 -470694.421790 27417.130745 -470694.329132 28011.392432 -470694.237751 29119.091906 -470694.145936 30233.760897 -470694.145936 31033.140496 -470682.197438 Overall Time for 1 Inference 31033.215601 Likelihood : -470682.197438 Parsimony starting tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_parsimonyTree.nucleic_M4058_406x6016_2008.phy_RAXML Final tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_result.nucleic_M4058_406x6016_2008.phy_RAXML Execution Log File written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_log.nucleic_M4058_406x6016_2008.phy_RAXML Execution information file written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_info.nucleic_M4058_406x6016_2008.phy_RAXML