IMPORTANT WARNING: Alignment column 1137 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1243 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1244 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1252 contains only undetermined values which will be treated as missing data

IMPORTANT WARNING
Found 4 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_M2945_62x1271_2006.phy.reduced


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

Alignment has 935 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.174793

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): 0.247324 pi(C): 0.270514 pi(G): 0.267915 pi(T): 0.214246



2.599636 -35481.153657
5.309621 -35411.404806
14.623731 -35238.665202
29.145645 -35182.657483
45.390729 -35175.801361
61.557447 -35173.914981
77.943372 -35168.581097
97.813582 -35165.741970
116.995697 -35164.297876
135.358447 -35163.714964
153.025407 -35163.618729
169.201778 -35163.525561
183.814353 -35163.435113
184.410651 -35163.435113
203.567276 -35107.009668


Overall Time for 1 Inference 203.584357
Likelihood   : -35107.009668


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2945_62x1271_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2945_62x1271_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2945_62x1271_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2945_62x1271_2006.phy_RAXML