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

                . Sequence filename : 				 nucleic_M2627_54x1915_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_M2627_54x1915_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 1299 patterns found. (out of a total of 1915 sites) 

. 625 sites without polymorphism (32.64%).

. Reading tree...

. This analysis requires at least 36Mo of memory space.

. (    1 sec) [    -37306.7530] [Branch lengths     ]
. (    3 sec) [    -36377.2234] [GTR parameters     ]
. (    3 sec) [    -36246.5829] [Alpha              ][  0.594698]
. (    4 sec) [    -36238.1568] [Branch lengths     ]
. (   11 sec) [    -35306.4601] [GTR parameters     ]
. (   12 sec) [    -35290.7769] [Alpha              ][  0.497967]
. (   13 sec) [    -35274.4047] [Branch lengths     ]
. (   19 sec) [    -35270.9173] [GTR parameters     ]
. (   19 sec) [    -35270.8547] [Alpha              ][  0.492312]
. (   20 sec) [    -35265.1551] [Branch lengths     ]
. (   24 sec) [    -35264.7412] [GTR parameters     ]
. (   25 sec) [    -35264.7037] [Alpha              ][  0.496543]
. (   26 sec) [    -35261.8553] [Branch lengths     ]
. (   30 sec) [    -35261.7087] [GTR parameters     ]
. (   30 sec) [    -35261.6981] [Alpha              ][  0.498769]
. (   31 sec) [    -35260.2160] [Branch lengths     ]
. (   35 sec) [    -35260.1439] [GTR parameters     ]
. (   35 sec) [    -35260.1413] [Alpha              ][  0.499847]
. (   36 sec) [    -35259.3583] [Branch lengths     ]
. (   38 sec) [    -35259.3168] [GTR parameters     ]
. (   38 sec) [    -35259.3165] [Alpha              ][  0.500347]
. (   39 sec) [    -35258.8789] [Branch lengths     ]
. (   40 sec) [    -35258.8548] [GTR parameters     ]
. (   40 sec) [    -35258.8548] [Alpha              ][  0.500347]
. (   42 sec) [    -35258.6064] [Branch lengths     ]
. (   44 sec) [    -35258.5911] [GTR parameters     ]
. (   45 sec) [    -35258.5911] [Alpha              ][  0.500347]
. (   46 sec) [    -35258.4443] [Branch lengths     ]
. (   47 sec) [    -35258.4361] [GTR parameters     ]
. (   47 sec) [    -35258.4361] [Alpha              ][  0.500347]
. (   48 sec) [    -35258.3491] [Branch lengths     ]
. (   49 sec) [    -35258.3442] [GTR parameters     ]
. (   49 sec) [    -35258.3442] [Alpha              ][  0.500347]
. (   50 sec) [    -35258.2914] [Branch lengths     ]
. (   51 sec) [    -35258.2886] [GTR parameters     ]
. (   51 sec) [    -35258.2884] [Alpha              ][  0.499847]
. (   52 sec) [    -35258.2570] [Branch lengths     ]
. (   53 sec) [    -35258.2549] [GTR parameters     ]
. (   53 sec) [    -35258.2549] [Alpha              ][  0.499847]
. (   54 sec) [    -35258.2362] [Branch lengths     ]
. (   55 sec) [    -35258.2346] [GTR parameters     ]
. (   56 sec) [    -35258.2346] [Alpha              ][  0.499847]
. (   57 sec) [    -35258.2224] [Branch lengths     ]
. (   58 sec) [    -35258.2223] [GTR parameters     ]
. (   58 sec) [    -35258.2223] [Alpha              ][  0.499847]
. (   59 sec) [    -35258.2159] [Branch lengths     ]
. (   60 sec) [    -35258.2146] [GTR parameters     ]
. (   60 sec) [    -35258.2146] [Alpha              ][  0.499847]
. (   61 sec) [    -35258.2100] [Branch lengths     ]
. (   62 sec) [    -35258.2098] [GTR parameters     ]
. (   62 sec) [    -35258.2098] [Alpha              ][  0.499847]
. (   63 sec) [    -35258.2072] [Branch lengths     ]
. (   64 sec) [    -35258.2068] [GTR parameters     ]
. (   64 sec) [    -35258.2068] [Alpha              ][  0.499847]
. (   65 sec) [    -35258.2050] [Branch lengths     ]
. (   66 sec) [    -35258.2050] [GTR parameters     ]
. (   66 sec) [    -35258.2050] [Alpha              ][  0.499847]
. (   67 sec) [    -35258.2041] [Branch lengths     ]
. (   68 sec) [    -35258.2038] [GTR parameters     ]
. (   68 sec) [    -35258.2038] [Alpha              ][  0.499847]
. (   69 sec) [    -35258.2031] [Branch lengths     ]
. (   70 sec) [    -35258.2031] [GTR parameters     ]
. (   70 sec) [    -35258.2031] [Alpha              ][  0.499847]
. (   71 sec) [    -35258.2031] [GTR parameters     ]
. (   71 sec) [    -35258.2031] [Alpha              ][  0.499847]
. Log likelihood of the current tree: -35258.203115.

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

. Printing the most likely tree in file 'nucleic_M2627_54x1915_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)