IMPORTANT WARNING: Alignment column 5001 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5069 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5070 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5071 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5072 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5073 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5074 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5075 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5076 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5077 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5078 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5079 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6012 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6013 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6014 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6015 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6016 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6017 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6018 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6019 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6020 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6021 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6022 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6023 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6024 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6025 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6026 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6027 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6028 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6029 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6030 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6031 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6032 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6033 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6034 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6035 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6036 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6037 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6038 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6039 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6040 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6041 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6042 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6043 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6044 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6045 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6046 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6047 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6048 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6049 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6050 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6051 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6052 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6053 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6054 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6055 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6056 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6057 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6074 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6075 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6076 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6077 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6078 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6079 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6080 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 65 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_M4055_306x7062_2008.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 6303 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.829353 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): 0.276471 pi(C): 0.227691 pi(G): 0.251661 pi(T): 0.244177 234.511470 -284777.930681 337.871248 -283875.670472 667.929307 -283720.774649 1346.364991 -283579.139032 2325.314221 -283492.734605 3578.351723 -282866.328142 4427.949245 -282267.626918 5081.370321 -282131.971276 5612.308008 -282064.689500 6100.432714 -282043.950262 6522.247484 -282039.425643 6919.226143 -282036.345814 7309.217297 -282034.106795 7688.032886 -282032.206422 8081.012628 -282024.127750 8468.981414 -282018.520109 8851.526216 -282015.870560 9235.959407 -282014.527863 9617.387739 -282013.519159 10014.195445 -282008.529660 10414.755099 -282007.639189 11187.718949 -281995.183606 11874.888857 -281993.374341 12541.546641 -281991.769089 13141.492629 -281990.822490 13744.120545 -281990.510915 14292.423355 -281990.310724 15087.207454 -281990.111504 16067.280522 -281990.111504 16780.939958 -281972.378924 Overall Time for 1 Inference 16781.013239 Likelihood : -281972.378924 Parsimony starting tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_parsimonyTree.nucleic_M4055_306x7062_2008.phy_RAXML Final tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_result.nucleic_M4055_306x7062_2008.phy_RAXML Execution Log File written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_log.nucleic_M4055_306x7062_2008.phy_RAXML Execution information file written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_info.nucleic_M4055_306x7062_2008.phy_RAXML