..........................                                      
 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 (nucleic_M2606_110x1206_2006.phy_FAST_TREE)"
                . 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) [    -29730.5430] [Branch lengths     ]
. (    3 sec) [    -28621.1165] [GTR parameters     ]
. (    3 sec) [    -28282.8808] [Alpha              ][  0.500960]
. (    4 sec) [    -28278.6679] [Branch lengths     ]
. (   10 sec) [    -27059.7301] [GTR parameters     ]
. (   11 sec) [    -27016.4370] [Alpha              ][  0.367417]
. (   12 sec) [    -26997.7163] [Branch lengths     ]
. (   17 sec) [    -26996.5751] [GTR parameters     ]
. (   17 sec) [    -26994.1772] [Alpha              ][  0.341154]
. (   18 sec) [    -26988.7708] [Branch lengths     ]
. (   22 sec) [    -26988.6795] [GTR parameters     ]
. (   23 sec) [    -26987.4226] [Alpha              ][  0.322920]
. (   24 sec) [    -26985.2552] [Branch lengths     ]
. (   28 sec) [    -26985.2262] [GTR parameters     ]
. (   28 sec) [    -26984.6356] [Alpha              ][  0.310866]
. (   30 sec) [    -26983.7099] [Branch lengths     ]
. (   34 sec) [    -26983.6974] [GTR parameters     ]
. (   34 sec) [    -26983.4218] [Alpha              ][  0.302885]
. (   35 sec) [    -26983.0237] [Branch lengths     ]
. (   39 sec) [    -26983.0196] [GTR parameters     ]
. (   40 sec) [    -26982.8952] [Alpha              ][  0.297392]
. (   41 sec) [    -26982.7192] [Branch lengths     ]
. (   45 sec) [    -26982.7169] [GTR parameters     ]
. (   45 sec) [    -26982.6654] [Alpha              ][  0.293889]
. (   47 sec) [    -26982.5922] [Branch lengths     ]
. (   50 sec) [    -26982.5912] [GTR parameters     ]
. (   51 sec) [    -26982.5703] [Alpha              ][  0.291666]
. (   52 sec) [    -26982.5404] [Branch lengths     ]
. (   54 sec) [    -26982.5399] [GTR parameters     ]
. (   55 sec) [    -26982.5312] [Alpha              ][  0.290233]
. (   56 sec) [    -26982.5190] [Branch lengths     ]
. (   57 sec) [    -26982.5189] [GTR parameters     ]
. (   57 sec) [    -26982.5154] [Alpha              ][  0.289322]
. (   58 sec) [    -26982.5106] [Branch lengths     ]
. (   59 sec) [    -26982.5106] [GTR parameters     ]
. (   60 sec) [    -26982.5094] [Alpha              ][  0.288768]
. (   61 sec) [    -26982.5075] [Branch lengths     ]
. (   62 sec) [    -26982.5074] [GTR parameters     ]
. (   62 sec) [    -26982.5069] [Alpha              ][  0.288420]
. (   63 sec) [    -26982.5061] [Branch lengths     ]
. (   66 sec) [    -26982.5059] [GTR parameters     ]
. (   66 sec) [    -26982.5056] [Alpha              ][  0.288131]
. (   67 sec) [    -26982.5053] [Branch lengths     ]
. (   69 sec) [    -26982.5052] [GTR parameters     ]
. (   69 sec) [    -26982.5052] [Alpha              ][  0.288131]
. (   71 sec) [    -26982.5052] [GTR parameters     ]
. (   72 sec) [    -26982.5052] [Alpha              ][  0.288131]
. Log likelihood of the current tree: -26982.505153.

. 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 0h1m40s

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)