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

                . Sequence filename : 				 nucleic_M2711_123x1181_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 (RAxML_result.nucleic_M2711_123x1181_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')...

. Compressing sequences...

. 617 patterns found. (out of a total of 1181 sites) 

. 633 sites without polymorphism (53.60%).

. Reading tree...

. This analysis requires at least 40Mo of memory space.

. (    1 sec) [    -11249.4727] [Branch lengths     ]
. (   11 sec) [    -10935.5530] [GTR parameters     ]
. (   11 sec) [    -10735.2276] [Alpha              ][  0.500960]
. (   12 sec) [    -10724.6426] [Branch lengths     ]
. (   18 sec) [    -10723.6285] [GTR parameters     ]
. (   18 sec) [    -10661.7130] [Alpha              ][  0.282715]
. (   19 sec) [    -10658.3691] [Branch lengths     ]
. (   24 sec) [    -10657.3698] [GTR parameters     ]
. (   25 sec) [    -10657.1468] [Alpha              ][  0.273808]
. (   26 sec) [    -10656.5192] [Branch lengths     ]
. (   32 sec) [    -10656.4974] [GTR parameters     ]
. (   32 sec) [    -10656.4974] [Alpha              ][  0.273808]
. (   33 sec) [    -10656.3486] [Branch lengths     ]
. (   36 sec) [    -10656.3472] [GTR parameters     ]
. (   37 sec) [    -10656.3471] [Alpha              ][  0.274082]
. (   38 sec) [    -10656.3192] [Branch lengths     ]
. (   39 sec) [    -10656.3191] [GTR parameters     ]
. (   39 sec) [    -10656.3191] [Alpha              ][  0.274082]
. (   40 sec) [    -10656.3129] [Branch lengths     ]
. (   41 sec) [    -10656.3129] [GTR parameters     ]
. (   41 sec) [    -10656.3129] [Alpha              ][  0.274082]
. (   42 sec) [    -10656.3118] [Branch lengths     ]
. (   44 sec) [    -10656.3116] [GTR parameters     ]
. (   44 sec) [    -10656.3116] [Alpha              ][  0.274082]
. (   45 sec) [    -10656.3113] [Branch lengths     ]
. (   46 sec) [    -10656.3113] [GTR parameters     ]
. (   46 sec) [    -10656.3113] [Alpha              ][  0.274082]
. (   48 sec) [    -10656.3113] [GTR parameters     ]
. (   48 sec) [    -10656.3113] [Alpha              ][  0.274082]
. Log likelihood of the current tree: -10656.311293.

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

. Printing the most likely tree in file 'nucleic_M2711_123x1181_2006.phy_phyml_tree.txt'...


. Time used 0h1m15s

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)