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

                . Sequence filename : 				 proteic_M2363_38x251_2004.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_M2363_38x251_2004.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 244 patterns found. (out of a total of 251 sites) 

. 24 sites without polymorphism (9.56%).

. Reading tree...

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

. (    1 sec) [    -11786.9813] [Branch lengths     ]
. (    2 sec) [    -11743.2199] [Alpha              ][  1.996970]
. (    3 sec) [    -11741.5086] [Branch lengths     ]
. (    4 sec) [    -11723.3104] [Alpha              ][  3.988404]
. (    5 sec) [    -11720.6788] [Branch lengths     ]
. (    6 sec) [    -11718.6743] [Alpha              ][  5.372883]
. (    7 sec) [    -11717.3932] [Branch lengths     ]
. (    7 sec) [    -11717.1403] [Alpha              ][  6.035312]
. (    8 sec) [    -11716.6926] [Branch lengths     ]
. (    9 sec) [    -11716.6555] [Alpha              ][  6.323908]
. (   10 sec) [    -11716.5160] [Branch lengths     ]
. (   10 sec) [    -11716.5104] [Alpha              ][  6.437855]
. (   11 sec) [    -11716.4717] [Branch lengths     ]
. (   12 sec) [    -11716.4705] [Alpha              ][  6.494144]
. (   13 sec) [    -11716.4606] [Branch lengths     ]
. (   13 sec) [    -11716.4604] [Alpha              ][  6.515006]
. (   14 sec) [    -11716.4576] [Branch lengths     ]
. (   15 sec) [    -11716.4576] [Alpha              ][  6.524635]
. (   16 sec) [    -11716.4567] [Branch lengths     ]
. (   16 sec) [    -11716.4566] [Alpha              ][  6.531159]
. (   17 sec) [    -11716.4566] [Alpha              ][  6.531159]
. Log likelihood of the current tree: -11716.456640.

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

. Printing the most likely tree in file 'proteic_M2363_38x251_2004.phy_phyml_tree.txt'...


. Time used 0h0m44s

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)