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

                . Sequence filename : 				 proteic_M1487_52x981_2003.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_M1487_52x981_2003.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 623 patterns found. (out of a total of 981 sites) 

. 470 sites without polymorphism (47.91%).

. Reading tree...

. This analysis requires at least 78Mo of memory space.

. (    4 sec) [    -16467.3451] [Branch lengths     ]
. (    7 sec) [    -16303.6623] [Alpha              ][  0.500960]
. (   11 sec) [    -16299.5332] [Branch lengths     ]
. (   12 sec) [    -16284.0972] [Alpha              ][  0.383143]
. (   16 sec) [    -16283.5083] [Branch lengths     ]
. (   17 sec) [    -16283.5016] [Alpha              ][  0.380921]
. (   21 sec) [    -16283.3602] [Branch lengths     ]
. (   22 sec) [    -16283.3572] [Alpha              ][  0.379421]
. (   26 sec) [    -16283.3142] [Branch lengths     ]
. (   27 sec) [    -16283.3128] [Alpha              ][  0.378389]
. (   31 sec) [    -16283.2976] [Branch lengths     ]
. (   32 sec) [    -16283.2972] [Alpha              ][  0.377768]
. (   35 sec) [    -16283.2920] [Branch lengths     ]
. (   37 sec) [    -16283.2919] [Alpha              ][  0.377390]
. (   40 sec) [    -16283.2900] [Branch lengths     ]
. (   41 sec) [    -16283.2900] [Alpha              ][  0.377390]
. (   45 sec) [    -16283.2895] [Branch lengths     ]
. (   46 sec) [    -16283.2894] [Alpha              ][  0.377013]
. (   48 sec) [    -16283.2894] [Alpha              ][  0.377013]
. Log likelihood of the current tree: -16283.289406.

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

. Printing the most likely tree in file 'proteic_M1487_52x981_2003.phy_phyml_tree.txt'...


. Time used 0h1m52s

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)