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

                . Sequence filename : 				 proteic_M2479_30x627_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_M2479_30x627_2005.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 521 patterns found. (out of a total of 627 sites) 

. 123 sites without polymorphism (19.62%).

. Reading tree...

. This analysis requires at least 37Mo of memory space.

. (    2 sec) [    -18080.8519] [Branch lengths     ]
. (    2 sec) [    -18069.7651] [Alpha              ][  0.778049]
. (    4 sec) [    -18068.9188] [Branch lengths     ]
. (    4 sec) [    -18068.8853] [Alpha              ][  0.767089]
. (    6 sec) [    -18068.5615] [Branch lengths     ]
. (    6 sec) [    -18068.5533] [Alpha              ][  0.761679]
. (    8 sec) [    -18068.4547] [Branch lengths     ]
. (    8 sec) [    -18068.4512] [Alpha              ][  0.758152]
. (   10 sec) [    -18068.4143] [Branch lengths     ]
. (   10 sec) [    -18068.4132] [Alpha              ][  0.756142]
. (   11 sec) [    -18068.4026] [Branch lengths     ]
. (   12 sec) [    -18068.4022] [Alpha              ][  0.754947]
. (   14 sec) [    -18068.3983] [Branch lengths     ]
. (   14 sec) [    -18068.3982] [Alpha              ][  0.754192]
. (   16 sec) [    -18068.3971] [Branch lengths     ]
. (   17 sec) [    -18068.3971] [Alpha              ][  0.754192]
. (   19 sec) [    -18068.3967] [Branch lengths     ]
. (   20 sec) [    -18068.3967] [Alpha              ][  0.753438]
. (   21 sec) [    -18068.3967] [Alpha              ][  0.753438]
. Log likelihood of the current tree: -18068.396681.

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

. Printing the most likely tree in file 'proteic_M2479_30x627_2005.phy_phyml_tree.txt'...


. Time used 0h0m48s

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)