..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename : 				 proteic_M2304_31x429_2005.phy
                . Data type :             			 aa
                . Sequence format : 				 interleaved
                . Number of data sets : 			 1
                . Nb of bootstrapped data sets : 		 0
                . Compute approximate likelihood ratio test : 	 yes (SH-like branch supports)
                . Model name : 					 WAG
                . Proportion of invariable sites :		 0.000000
                . Number of subst. rate categs : 		 4
                . Gamma distribution parameter : 		 estimated
                . 'Middle' of each rate class  : 		 mean
                . Amino acid equilibrium frequencies : 		 model
                . Optimise tree topology : 			 no
                . Evaluted tree : 				 file "user tree (proteic_M2304_31x429_2005.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 35 sites are made from completely undetermined states ('X', '-', '?')...

. Compressing sequences...

. 305 patterns found. (out of a total of 429 sites) 

. 122 sites without polymorphism (28.44%).

. Reading tree...

. This analysis requires at least 23Mo of memory space.

. (    1 sec) [     -5506.1382] [Branch lengths     ]
. (    1 sec) [     -5506.1276] [Alpha              ][  1.017647]
. (    2 sec) [     -5506.0486] [Branch lengths     ]
. (    3 sec) [     -5506.0486] [Alpha              ][  1.017647]
. (    4 sec) [     -5506.0417] [Branch lengths     ]
. (    4 sec) [     -5506.0417] [Alpha              ][  1.016630]
. (    5 sec) [     -5506.0411] [Branch lengths     ]
. (    5 sec) [     -5506.0411] [Alpha              ][  1.016630]
. (    6 sec) [     -5506.0411] [Alpha              ][  1.016630]
. Log likelihood of the current tree: -5506.041063.

. Compute aLRT branch supports on the most likely tree...

. Printing the most likely tree in file 'proteic_M2304_31x429_2005.phy_phyml_tree.txt'...


. Time used 0h0m23s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
java.lang.NullPointerException
	at java.io.FileInputStream.<init>(FileInputStream.java:103)
	at java.io.FileReader.<init>(FileReader.java:55)
	at Recomp.<init>(Recomp.java:114)
	at Recomp.main(Recomp.java:52)