IMPORTANT WARNING: Alignment column 554 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 910 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1096 contains only undetermined values which will be treated as missing data

IMPORTANT WARNING
Found 3 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_M2944_80x1495_2006.phy.reduced


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

Alignment has 494 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.332751

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): 0.266579 pi(C): 0.210449 pi(G): 0.256293 pi(T): 0.266679



1.546947 -9107.547555
3.490802 -9087.270389
10.172332 -9036.861987
17.079011 -9021.396844
24.463844 -9018.394808
31.425966 -9017.866901
38.408227 -9017.666975
48.247690 -9017.578078
57.257539 -9017.425148
69.198494 -9017.331821
75.170296 -9017.331821
83.362047 -8993.390687


Overall Time for 1 Inference 83.381701
Likelihood   : -8993.390687


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2944_80x1495_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2944_80x1495_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2944_80x1495_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2944_80x1495_2006.phy_RAXML