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

                . Sequence filename : 				 nucleic_M2932_68x1712_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_M2932_68x1712_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 1264 patterns found. (out of a total of 1712 sites) 

. 601 sites without polymorphism (35.11%).

. Reading tree...

. This analysis requires at least 45Mo of memory space.

. (    2 sec) [    -15339.5570] [Branch lengths     ]
. (    9 sec) [    -14995.5550] [GTR parameters     ]
. (    9 sec) [    -14965.5739] [Alpha              ][  0.658658]
. (   10 sec) [    -14949.5249] [Branch lengths     ]
. (   16 sec) [    -14947.3109] [GTR parameters     ]
. (   17 sec) [    -14945.9566] [Alpha              ][  0.606766]
. (   18 sec) [    -14942.1977] [Branch lengths     ]
. (   23 sec) [    -14942.0274] [GTR parameters     ]
. (   23 sec) [    -14941.8585] [Alpha              ][  0.590037]
. (   25 sec) [    -14940.8783] [Branch lengths     ]
. (   27 sec) [    -14940.8438] [GTR parameters     ]
. (   28 sec) [    -14940.7886] [Alpha              ][  0.580445]
. (   29 sec) [    -14940.5356] [Branch lengths     ]
. (   34 sec) [    -14940.5132] [GTR parameters     ]
. (   35 sec) [    -14940.5003] [Alpha              ][  0.575859]
. (   36 sec) [    -14940.4265] [Branch lengths     ]
. (   38 sec) [    -14940.4243] [GTR parameters     ]
. (   39 sec) [    -14940.4207] [Alpha              ][  0.573435]
. (   40 sec) [    -14940.3971] [Branch lengths     ]
. (   44 sec) [    -14940.3962] [GTR parameters     ]
. (   44 sec) [    -14940.3955] [Alpha              ][  0.572323]
. (   46 sec) [    -14940.3854] [Branch lengths     ]
. (   49 sec) [    -14940.3851] [GTR parameters     ]
. (   49 sec) [    -14940.3850] [Alpha              ][  0.571750]
. (   50 sec) [    -14940.3785] [Branch lengths     ]
. (   51 sec) [    -14940.3784] [GTR parameters     ]
. (   52 sec) [    -14940.3784] [Alpha              ][  0.571750]
. (   53 sec) [    -14940.3732] [Branch lengths     ]
. (   55 sec) [    -14940.3731] [GTR parameters     ]
. (   55 sec) [    -14940.3731] [Alpha              ][  0.571178]
. (   56 sec) [    -14940.3680] [Branch lengths     ]
. (   57 sec) [    -14940.3680] [GTR parameters     ]
. (   57 sec) [    -14940.3680] [Alpha              ][  0.571178]
. (   59 sec) [    -14940.3630] [Branch lengths     ]
. (   60 sec) [    -14940.3630] [GTR parameters     ]
. (   60 sec) [    -14940.3630] [Alpha              ][  0.571178]
. (   61 sec) [    -14940.3580] [Branch lengths     ]
. (   63 sec) [    -14940.3580] [GTR parameters     ]
. (   63 sec) [    -14940.3580] [Alpha              ][  0.571178]
. (   64 sec) [    -14940.3534] [Branch lengths     ]
. (   66 sec) [    -14940.3534] [GTR parameters     ]
. (   66 sec) [    -14940.3534] [Alpha              ][  0.571178]
. (   68 sec) [    -14940.3489] [Branch lengths     ]
. (   69 sec) [    -14940.3489] [GTR parameters     ]
. (   69 sec) [    -14940.3489] [Alpha              ][  0.571178]
. (   71 sec) [    -14940.3459] [Branch lengths     ]
. (   72 sec) [    -14940.3459] [GTR parameters     ]
. (   72 sec) [    -14940.3459] [Alpha              ][  0.571178]
. (   73 sec) [    -14940.3456] [Branch lengths     ]
. (   74 sec) [    -14940.3456] [GTR parameters     ]
. (   75 sec) [    -14940.3456] [Alpha              ][  0.571178]
. (   75 sec) [    -14940.3456] [GTR parameters     ]
. (   76 sec) [    -14940.3456] [Alpha              ][  0.571178]
. Log likelihood of the current tree: -14940.345569.

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

. Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'...


. Time used 0h1m51s

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)