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

                . Sequence filename : 				 nucleic_M2662_60x1348_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_M2662_60x1348_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 664 patterns found. (out of a total of 1348 sites) 

. 794 sites without polymorphism (58.90%).

. Reading tree...

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

. (    0 sec) [    -13162.8302] [Branch lengths     ]
. (    5 sec) [    -12632.5349] [GTR parameters     ]
. (    5 sec) [    -12419.6388] [Alpha              ][  0.500960]
. (    5 sec) [    -12413.7214] [Branch lengths     ]
. (    8 sec) [    -12413.1833] [GTR parameters     ]
. (    8 sec) [    -12354.5277] [Alpha              ][  0.296735]
. (    8 sec) [    -12353.1299] [Branch lengths     ]
. (   11 sec) [    -12352.7900] [GTR parameters     ]
. (   11 sec) [    -12352.7817] [Alpha              ][  0.294905]
. (   11 sec) [    -12352.6383] [Branch lengths     ]
. (   12 sec) [    -12352.6367] [GTR parameters     ]
. (   12 sec) [    -12352.6360] [Alpha              ][  0.295384]
. (   13 sec) [    -12352.6036] [Branch lengths     ]
. (   13 sec) [    -12352.6036] [GTR parameters     ]
. (   13 sec) [    -12352.6034] [Alpha              ][  0.295680]
. (   14 sec) [    -12352.5954] [Branch lengths     ]
. (   14 sec) [    -12352.5951] [GTR parameters     ]
. (   14 sec) [    -12352.5951] [Alpha              ][  0.295680]
. (   15 sec) [    -12352.5930] [Branch lengths     ]
. (   16 sec) [    -12352.5928] [GTR parameters     ]
. (   16 sec) [    -12352.5928] [Alpha              ][  0.295680]
. (   16 sec) [    -12352.5922] [Branch lengths     ]
. (   17 sec) [    -12352.5922] [GTR parameters     ]
. (   17 sec) [    -12352.5922] [Alpha              ][  0.295680]
. (   17 sec) [    -12352.5922] [GTR parameters     ]
. (   17 sec) [    -12352.5922] [Alpha              ][  0.295680]
. Log likelihood of the current tree: -12352.592232.

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

. Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'...


. Time used 0h0m34s

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)