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

                . Sequence filename : 				 nucleic_M2856_61x970_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_M2856_61x970_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 686 patterns found. (out of a total of 970 sites) 

. 322 sites without polymorphism (33.20%).

. Reading tree...

. This analysis requires at least 22Mo of memory space.

. (    1 sec) [    -26355.5623] [Branch lengths     ]
. (    2 sec) [    -25679.9399] [GTR parameters     ]
. (    2 sec) [    -25449.5042] [Alpha              ][  0.500960]
. (    3 sec) [    -25440.3652] [Branch lengths     ]
. (    7 sec) [    -25157.7777] [GTR parameters     ]
. (    7 sec) [    -25144.9868] [Alpha              ][  0.421539]
. (    8 sec) [    -25132.6772] [Branch lengths     ]
. (   12 sec) [    -25129.7473] [GTR parameters     ]
. (   12 sec) [    -25129.6826] [Alpha              ][  0.416663]
. (   13 sec) [    -25124.9334] [Branch lengths     ]
. (   16 sec) [    -25124.4486] [GTR parameters     ]
. (   16 sec) [    -25124.4460] [Alpha              ][  0.417637]
. (   17 sec) [    -25122.3260] [Branch lengths     ]
. (   19 sec) [    -25122.1421] [GTR parameters     ]
. (   19 sec) [    -25122.1398] [Alpha              ][  0.418568]
. (   20 sec) [    -25121.2649] [Branch lengths     ]
. (   22 sec) [    -25121.1909] [GTR parameters     ]
. (   22 sec) [    -25121.1909] [Alpha              ][  0.418568]
. (   23 sec) [    -25120.7128] [Branch lengths     ]
. (   24 sec) [    -25120.6735] [GTR parameters     ]
. (   24 sec) [    -25120.6731] [Alpha              ][  0.418986]
. (   25 sec) [    -25120.4448] [Branch lengths     ]
. (   27 sec) [    -25120.4272] [GTR parameters     ]
. (   27 sec) [    -25120.4272] [Alpha              ][  0.418986]
. (   27 sec) [    -25120.2875] [Branch lengths     ]
. (   29 sec) [    -25120.2778] [GTR parameters     ]
. (   29 sec) [    -25120.2778] [Alpha              ][  0.418986]
. (   30 sec) [    -25120.2088] [Branch lengths     ]
. (   32 sec) [    -25120.2027] [GTR parameters     ]
. (   32 sec) [    -25120.2027] [Alpha              ][  0.418986]
. (   33 sec) [    -25120.1642] [Branch lengths     ]
. (   34 sec) [    -25120.1608] [GTR parameters     ]
. (   34 sec) [    -25120.1608] [Alpha              ][  0.418986]
. (   35 sec) [    -25120.1458] [Branch lengths     ]
. (   36 sec) [    -25120.1424] [GTR parameters     ]
. (   36 sec) [    -25120.1424] [Alpha              ][  0.418986]
. (   37 sec) [    -25120.1322] [Branch lengths     ]
. (   38 sec) [    -25120.1321] [GTR parameters     ]
. (   38 sec) [    -25120.1321] [Alpha              ][  0.418986]
. (   38 sec) [    -25120.1284] [Branch lengths     ]
. (   39 sec) [    -25120.1256] [GTR parameters     ]
. (   40 sec) [    -25120.1256] [Alpha              ][  0.418986]
. (   40 sec) [    -25120.1221] [Branch lengths     ]
. (   41 sec) [    -25120.1217] [GTR parameters     ]
. (   41 sec) [    -25120.1217] [Alpha              ][  0.418986]
. (   42 sec) [    -25120.1198] [Branch lengths     ]
. (   42 sec) [    -25120.1197] [GTR parameters     ]
. (   43 sec) [    -25120.1197] [Alpha              ][  0.418986]
. (   43 sec) [    -25120.1189] [Branch lengths     ]
. (   45 sec) [    -25120.1181] [GTR parameters     ]
. (   45 sec) [    -25120.1181] [Alpha              ][  0.418986]
. (   46 sec) [    -25120.1173] [Branch lengths     ]
. (   46 sec) [    -25120.1173] [GTR parameters     ]
. (   46 sec) [    -25120.1173] [Alpha              ][  0.418986]
. (   47 sec) [    -25120.1173] [GTR parameters     ]
. (   47 sec) [    -25120.1173] [Alpha              ][  0.418986]
. Log likelihood of the current tree: -25120.117273.

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

. Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'...


. Time used 0h1m5s

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)