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

                . Sequence filename : 				 proteic_M2558_27x1060_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_M2558_27x1060_2005.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 746 patterns found. (out of a total of 1060 sites) 

. 362 sites without polymorphism (34.15%).

. Reading tree...

. This analysis requires at least 47Mo of memory space.

. (    2 sec) [    -37279.9173] [Branch lengths     ]
. (    3 sec) [    -37243.8229] [Alpha              ][  0.725919]
. (    5 sec) [    -37228.0321] [Branch lengths     ]
. (    6 sec) [    -37227.3165] [Alpha              ][  0.694905]
. (    8 sec) [    -37217.1757] [Branch lengths     ]
. (    9 sec) [    -37216.3282] [Alpha              ][  0.662605]
. (   11 sec) [    -37209.7998] [Branch lengths     ]
. (   12 sec) [    -37209.1481] [Alpha              ][  0.635427]
. (   14 sec) [    -37205.2762] [Branch lengths     ]
. (   14 sec) [    -37204.6119] [Alpha              ][  0.609056]
. (   16 sec) [    -37202.1966] [Branch lengths     ]
. (   17 sec) [    -37201.7912] [Alpha              ][  0.589229]
. (   19 sec) [    -37200.3418] [Branch lengths     ]
. (   20 sec) [    -37199.9983] [Alpha              ][  0.571566]
. (   22 sec) [    -37199.0887] [Branch lengths     ]
. (   22 sec) [    -37198.8946] [Alpha              ][  0.558741]
. (   24 sec) [    -37198.3455] [Branch lengths     ]
. (   25 sec) [    -37198.1886] [Alpha              ][  0.547496]
. (   27 sec) [    -37197.8415] [Branch lengths     ]
. (   28 sec) [    -37197.7562] [Alpha              ][  0.539471]
. (   29 sec) [    -37197.5460] [Branch lengths     ]
. (   30 sec) [    -37197.4777] [Alpha              ][  0.531906]
. (   32 sec) [    -37197.3352] [Branch lengths     ]
. (   33 sec) [    -37197.3022] [Alpha              ][  0.526694]
. (   35 sec) [    -37197.2150] [Branch lengths     ]
. (   35 sec) [    -37197.1895] [Alpha              ][  0.522144]
. (   37 sec) [    -37197.1337] [Branch lengths     ]
. (   38 sec) [    -37197.1210] [Alpha              ][  0.518939]
. (   40 sec) [    -37197.0871] [Branch lengths     ]
. (   41 sec) [    -37197.0771] [Alpha              ][  0.516114]
. (   42 sec) [    -37197.0554] [Branch lengths     ]
. (   44 sec) [    -37197.0505] [Alpha              ][  0.514128]
. (   45 sec) [    -37197.0373] [Branch lengths     ]
. (   46 sec) [    -37197.0334] [Alpha              ][  0.512358]
. (   48 sec) [    -37197.0250] [Branch lengths     ]
. (   49 sec) [    -37197.0231] [Alpha              ][  0.511126]
. (   50 sec) [    -37197.0180] [Branch lengths     ]
. (   51 sec) [    -37197.0165] [Alpha              ][  0.510029]
. (   53 sec) [    -37197.0132] [Branch lengths     ]
. (   54 sec) [    -37197.0126] [Alpha              ][  0.509260]
. (   56 sec) [    -37197.0105] [Branch lengths     ]
. (   56 sec) [    -37197.0100] [Alpha              ][  0.508573]
. (   58 sec) [    -37197.0087] [Branch lengths     ]
. (   59 sec) [    -37197.0085] [Alpha              ][  0.508064]
. (   60 sec) [    -37197.0077] [Branch lengths     ]
. (   61 sec) [    -37197.0075] [Alpha              ][  0.507556]
. (   62 sec) [    -37197.0075] [Alpha              ][  0.507556]
. Log likelihood of the current tree: -37197.007531.

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

. Printing the most likely tree in file 'proteic_M2558_27x1060_2005.phy_phyml_tree.txt'...


. Time used 0h1m46s

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)