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

                . Sequence filename : 				 nucleic_M2733_60x1207_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_M2733_60x1207_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 564 patterns found. (out of a total of 1207 sites) 

. 771 sites without polymorphism (63.88%).

. Reading tree...

. This analysis requires at least 18Mo of memory space.

. (    1 sec) [    -11730.1017] [Branch lengths     ]
. (    3 sec) [    -11309.5479] [GTR parameters     ]
. (    3 sec) [    -11073.1038] [Alpha              ][  0.500960]
. (    4 sec) [    -11069.2074] [Branch lengths     ]
. (    5 sec) [    -11066.9741] [GTR parameters     ]
. (    5 sec) [    -10957.7626] [Alpha              ][  0.250961]
. (    6 sec) [    -10956.1501] [Branch lengths     ]
. (    7 sec) [    -10953.8369] [GTR parameters     ]
. (    7 sec) [    -10951.1641] [Alpha              ][  0.224231]
. (    8 sec) [    -10950.5843] [Branch lengths     ]
. (    9 sec) [    -10950.5161] [GTR parameters     ]
. (    9 sec) [    -10950.4397] [Alpha              ][  0.220056]
. (    9 sec) [    -10950.3303] [Branch lengths     ]
. (   10 sec) [    -10950.3295] [GTR parameters     ]
. (   10 sec) [    -10950.3201] [Alpha              ][  0.218518]
. (   10 sec) [    -10950.3017] [Branch lengths     ]
. (   11 sec) [    -10950.3016] [GTR parameters     ]
. (   11 sec) [    -10950.3005] [Alpha              ][  0.217979]
. (   11 sec) [    -10950.2971] [Branch lengths     ]
. (   12 sec) [    -10950.2971] [GTR parameters     ]
. (   12 sec) [    -10950.2970] [Alpha              ][  0.217761]
. (   12 sec) [    -10950.2964] [Branch lengths     ]
. (   13 sec) [    -10950.2964] [GTR parameters     ]
. (   13 sec) [    -10950.2964] [Alpha              ][  0.217761]
. (   13 sec) [    -10950.2964] [GTR parameters     ]
. (   13 sec) [    -10950.2964] [Alpha              ][  0.217761]
. Log likelihood of the current tree: -10950.296375.

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

. Printing the most likely tree in file 'nucleic_M2733_60x1207_2006.phy_phyml_tree.txt'...


. Time used 0h0m30s

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)