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

                . Sequence filename : 				 nucleic_M2588_68x1196_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_M2588_68x1196_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 730 patterns found. (out of a total of 1196 sites) 

. 526 sites without polymorphism (43.98%).

. Reading tree...

. This analysis requires at least 26Mo of memory space.

. (    1 sec) [    -12885.8870] [Branch lengths     ]
. (    7 sec) [    -12293.2923] [GTR parameters     ]
. (    8 sec) [    -12107.4334] [Alpha              ][  0.500960]
. (    9 sec) [    -12084.5218] [Branch lengths     ]
. (   12 sec) [    -12080.2557] [GTR parameters     ]
. (   12 sec) [    -12040.1317] [Alpha              ][  0.325721]
. (   13 sec) [    -12032.6778] [Branch lengths     ]
. (   17 sec) [    -12030.2930] [GTR parameters     ]
. (   17 sec) [    -12029.7045] [Alpha              ][  0.310006]
. (   17 sec) [    -12027.6848] [Branch lengths     ]
. (   21 sec) [    -12027.4863] [GTR parameters     ]
. (   21 sec) [    -12027.3850] [Alpha              ][  0.303879]
. (   22 sec) [    -12026.1084] [Branch lengths     ]
. (   24 sec) [    -12026.0545] [GTR parameters     ]
. (   24 sec) [    -12026.0518] [Alpha              ][  0.304851]
. (   25 sec) [    -12025.4377] [Branch lengths     ]
. (   30 sec) [    -12025.4159] [GTR parameters     ]
. (   31 sec) [    -12025.4083] [Alpha              ][  0.303079]
. (   31 sec) [    -12025.1971] [Branch lengths     ]
. (   34 sec) [    -12025.1937] [GTR parameters     ]
. (   34 sec) [    -12025.1926] [Alpha              ][  0.303674]
. (   35 sec) [    -12025.0965] [Branch lengths     ]
. (   36 sec) [    -12025.0936] [GTR parameters     ]
. (   37 sec) [    -12025.0931] [Alpha              ][  0.303149]
. (   37 sec) [    -12025.0551] [Branch lengths     ]
. (   40 sec) [    -12025.0510] [GTR parameters     ]
. (   41 sec) [    -12025.0510] [Alpha              ][  0.303149]
. (   41 sec) [    -12025.0327] [Branch lengths     ]
. (   42 sec) [    -12025.0325] [GTR parameters     ]
. (   42 sec) [    -12025.0325] [Alpha              ][  0.303149]
. (   43 sec) [    -12025.0248] [Branch lengths     ]
. (   44 sec) [    -12025.0245] [GTR parameters     ]
. (   44 sec) [    -12025.0245] [Alpha              ][  0.303149]
. (   45 sec) [    -12025.0206] [Branch lengths     ]
. (   47 sec) [    -12025.0202] [GTR parameters     ]
. (   47 sec) [    -12025.0202] [Alpha              ][  0.302846]
. (   48 sec) [    -12025.0183] [Branch lengths     ]
. (   49 sec) [    -12025.0182] [GTR parameters     ]
. (   49 sec) [    -12025.0182] [Alpha              ][  0.302846]
. (   50 sec) [    -12025.0174] [Branch lengths     ]
. (   52 sec) [    -12025.0172] [GTR parameters     ]
. (   52 sec) [    -12025.0172] [Alpha              ][  0.302846]
. (   53 sec) [    -12025.0168] [Branch lengths     ]
. (   55 sec) [    -12025.0163] [GTR parameters     ]
. (   55 sec) [    -12025.0163] [Alpha              ][  0.302846]
. (   56 sec) [    -12025.0163] [GTR parameters     ]
. (   56 sec) [    -12025.0163] [Alpha              ][  0.302846]
. Log likelihood of the current tree: -12025.016268.

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

. Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'...


. Time used 0h1m13s

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)