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

                . Sequence filename : 				 nucleic_M2606_110x1206_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_M2606_110x1206_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 662 patterns found. (out of a total of 1206 sites) 

. 540 sites without polymorphism (44.78%).

. Reading tree...

. This analysis requires at least 38Mo of memory space.

. (    1 sec) [    -29717.6244] [Branch lengths     ]
. (    2 sec) [    -28614.3818] [GTR parameters     ]
. (    3 sec) [    -28270.9606] [Alpha              ][  0.500960]
. (    4 sec) [    -28265.0528] [Branch lengths     ]
. (   11 sec) [    -27028.0484] [GTR parameters     ]
. (   11 sec) [    -26983.4004] [Alpha              ][  0.365140]
. (   12 sec) [    -26962.7642] [Branch lengths     ]
. (   17 sec) [    -26961.6382] [GTR parameters     ]
. (   17 sec) [    -26958.2706] [Alpha              ][  0.334124]
. (   18 sec) [    -26953.7527] [Branch lengths     ]
. (   22 sec) [    -26953.6608] [GTR parameters     ]
. (   23 sec) [    -26952.5272] [Alpha              ][  0.317026]
. (   24 sec) [    -26950.7530] [Branch lengths     ]
. (   28 sec) [    -26950.7316] [GTR parameters     ]
. (   28 sec) [    -26950.2328] [Alpha              ][  0.306091]
. (   29 sec) [    -26949.4950] [Branch lengths     ]
. (   33 sec) [    -26949.4863] [GTR parameters     ]
. (   33 sec) [    -26949.2655] [Alpha              ][  0.298743]
. (   34 sec) [    -26948.9488] [Branch lengths     ]
. (   38 sec) [    -26948.9444] [GTR parameters     ]
. (   38 sec) [    -26948.8538] [Alpha              ][  0.294091]
. (   40 sec) [    -26948.7227] [Branch lengths     ]
. (   42 sec) [    -26948.7218] [GTR parameters     ]
. (   42 sec) [    -26948.6845] [Alpha              ][  0.291126]
. (   43 sec) [    -26948.6318] [Branch lengths     ]
. (   46 sec) [    -26948.6306] [GTR parameters     ]
. (   46 sec) [    -26948.6154] [Alpha              ][  0.289234]
. (   47 sec) [    -26948.5938] [Branch lengths     ]
. (   49 sec) [    -26948.5936] [GTR parameters     ]
. (   49 sec) [    -26948.5874] [Alpha              ][  0.288025]
. (   50 sec) [    -26948.5789] [Branch lengths     ]
. (   52 sec) [    -26948.5787] [GTR parameters     ]
. (   52 sec) [    -26948.5764] [Alpha              ][  0.287275]
. (   54 sec) [    -26948.5729] [Branch lengths     ]
. (   56 sec) [    -26948.5728] [GTR parameters     ]
. (   56 sec) [    -26948.5719] [Alpha              ][  0.286797]
. (   57 sec) [    -26948.5705] [Branch lengths     ]
. (   58 sec) [    -26948.5704] [GTR parameters     ]
. (   59 sec) [    -26948.5701] [Alpha              ][  0.286484]
. (   60 sec) [    -26948.5695] [Branch lengths     ]
. (   61 sec) [    -26948.5695] [GTR parameters     ]
. (   61 sec) [    -26948.5694] [Alpha              ][  0.286198]
. (   64 sec) [    -26948.5693] [GTR parameters     ]
. (   64 sec) [    -26948.5693] [Alpha              ][  0.286198]
. Log likelihood of the current tree: -26948.569250.

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

. Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'...


. Time used 0h1m34s

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)