IMPORTANT WARNING: Alignment column 42 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 620 contains only undetermined values which will be treated as missing data

IMPORTANT WARNING
Found 2 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/ori_nucl_raxml/nucleic_M2702_54x886_2006.phy.reduced


You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008

Alignment has 382 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.068577

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): 0.252295 pi(C): 0.211521 pi(G): 0.306869 pi(T): 0.229316



0.548673 -5455.570197
1.433903 -5448.371431
3.220706 -5445.834417
6.092631 -5418.217176
9.511608 -5406.328579
13.612439 -5400.915147
17.321462 -5400.707099
21.328647 -5400.616440
25.424302 -5400.531940
29.484649 -5400.451282
30.290745 -5400.451282
33.853810 -5382.621586


Overall Time for 1 Inference 33.868914
Likelihood   : -5382.621586


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2702_54x886_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2702_54x886_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2702_54x886_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2702_54x886_2006.phy_RAXML