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

                . Sequence filename : 				 nucleic_M2738_53x1538_2006.phy
                . Data type :             			 dna
                . 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 : 					 GTR
                . Proportion of invariable sites :		 0.000000
                . Number of subst. rate categs : 		 4
                . Gamma distribution parameter : 		 estimated
                . 'Middle' of each rate class  : 		 mean
                . Nucleotide equilibrium frequencies : 		 empirical
                . Optimise tree topology : 			 no
                . Evaluted tree : 				 file "user tree (nucleic_M2738_53x1538_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 762 patterns found. (out of a total of 1538 sites) 

. 828 sites without polymorphism (53.84%).

. Reading tree...

. This analysis requires at least 21Mo of memory space.

. (    1 sec) [    -14860.8076] [Branch lengths     ]
. (    2 sec) [    -14637.7926] [GTR parameters     ]
. (    2 sec) [    -14421.7959] [Alpha              ][  0.500960]
. (    3 sec) [    -14416.8473] [Branch lengths     ]
. (    7 sec) [    -13975.8808] [GTR parameters     ]
. (    8 sec) [    -13921.8819] [Alpha              ][  0.308613]
. (    8 sec) [    -13914.5587] [Branch lengths     ]
. (   13 sec) [    -13912.9997] [GTR parameters     ]
. (   13 sec) [    -13912.7739] [Alpha              ][  0.299605]
. (   14 sec) [    -13912.1369] [Branch lengths     ]
. (   18 sec) [    -13912.1041] [GTR parameters     ]
. (   18 sec) [    -13912.1037] [Alpha              ][  0.299142]
. (   19 sec) [    -13912.0162] [Branch lengths     ]
. (   19 sec) [    -13912.0162] [GTR parameters     ]
. (   19 sec) [    -13912.0158] [Alpha              ][  0.299441]
. (   20 sec) [    -13912.0011] [Branch lengths     ]
. (   21 sec) [    -13912.0009] [GTR parameters     ]
. (   21 sec) [    -13912.0009] [Alpha              ][  0.299441]
. (   22 sec) [    -13911.9981] [Branch lengths     ]
. (   24 sec) [    -13911.9926] [GTR parameters     ]
. (   25 sec) [    -13911.9926] [Alpha              ][  0.299441]
. (   25 sec) [    -13911.9912] [Branch lengths     ]
. (   26 sec) [    -13911.9911] [GTR parameters     ]
. (   26 sec) [    -13911.9911] [Alpha              ][  0.299441]
. (   27 sec) [    -13911.9908] [Branch lengths     ]
. (   28 sec) [    -13911.9906] [GTR parameters     ]
. (   28 sec) [    -13911.9906] [Alpha              ][  0.299441]
. (   29 sec) [    -13911.9905] [GTR parameters     ]
. (   29 sec) [    -13911.9905] [Alpha              ][  0.299441]
. Log likelihood of the current tree: -13911.990540.

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

. Printing the most likely tree in file 'nucleic_M2738_53x1538_2006.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)