IMPORTANT WARNING: Alignment column 1 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 8 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 10 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 11 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 12 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 13 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 15 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 16 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 17 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 18 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 19 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 20 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 21 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 22 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 23 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 24 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 25 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 26 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 27 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 28 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 29 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 30 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 31 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 32 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 33 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 776 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1002 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1460 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1461 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1462 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1463 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1464 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1465 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1466 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1467 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1468 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1469 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1470 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1471 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1472 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1473 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1474 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1475 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1476 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1477 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1478 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1479 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1480 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1481 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1482 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1483 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1484 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1485 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1486 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1487 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1488 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1489 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1490 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1491 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1492 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1493 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1494 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1495 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1496 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1497 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1498 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1499 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1500 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1501 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1502 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1503 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1504 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1505 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1506 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1507 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1508 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1509 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1510 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1511 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1512 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1513 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1514 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1515 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1516 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1517 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1739 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1740 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1741 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1742 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1743 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1744 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1745 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1746 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1747 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1748 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1749 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1750 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1751 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1752 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1753 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1754 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1755 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1756 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1757 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1758 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1759 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1760 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1761 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1762 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2663 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 118 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_M4057_416x4150_2008.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 3510 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.711379 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): 0.261219 pi(C): 0.215280 pi(G): 0.292988 pi(T): 0.230513 121.004632 -166103.610782 191.051745 -165591.078974 400.610654 -165322.474815 817.555024 -165179.779256 1527.583009 -164738.447315 1953.115346 -164467.458913 2269.938899 -164271.368174 2544.959656 -164194.490407 2816.568742 -164158.322975 3085.440851 -164138.349700 3341.898688 -164132.218790 3580.713199 -164127.624783 3801.383843 -164111.560999 4018.797568 -164110.594309 4232.047247 -164110.385773 4760.182423 -164106.012802 5223.295127 -164102.829195 5694.357463 -164093.333971 6129.850314 -164092.690618 6588.920088 -164087.179497 7021.227993 -164086.964666 7452.151309 -164086.901798 7783.023709 -164086.838021 8399.494677 -164086.779029 9027.866130 -164086.779029 9438.955838 -164080.966342 Overall Time for 1 Inference 9439.001319 Likelihood : -164080.966342 Parsimony starting tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_parsimonyTree.nucleic_M4057_416x4150_2008.phy_RAXML Final tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_result.nucleic_M4057_416x4150_2008.phy_RAXML Execution Log File written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_log.nucleic_M4057_416x4150_2008.phy_RAXML Execution information file written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_info.nucleic_M4057_416x4150_2008.phy_RAXML