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

                . Sequence filename : 				 nucleic_M2564_142x1130_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_M2564_142x1130_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 780 patterns found. (out of a total of 1130 sites) 

. 486 sites without polymorphism (43.01%).

. Reading tree...

. This analysis requires at least 59Mo of memory space.

. (    2 sec) [    -21279.2624] [Branch lengths     ]
. (    9 sec) [    -20871.5318] [GTR parameters     ]
. (   10 sec) [    -20542.0378] [Alpha              ][  0.500960]
. (   12 sec) [    -20511.6466] [Branch lengths     ]
. (   16 sec) [    -20509.7236] [GTR parameters     ]
. (   16 sec) [    -20455.7745] [Alpha              ][  0.345396]
. (   18 sec) [    -20450.4795] [Branch lengths     ]
. (   22 sec) [    -20449.9488] [GTR parameters     ]
. (   22 sec) [    -20449.8602] [Alpha              ][  0.340648]
. (   24 sec) [    -20449.3912] [Branch lengths     ]
. (   26 sec) [    -20449.3806] [GTR parameters     ]
. (   26 sec) [    -20449.3805] [Alpha              ][  0.340988]
. (   28 sec) [    -20449.2669] [Branch lengths     ]
. (   29 sec) [    -20449.2658] [GTR parameters     ]
. (   29 sec) [    -20449.2658] [Alpha              ][  0.340988]
. (   31 sec) [    -20449.2374] [Branch lengths     ]
. (   32 sec) [    -20449.2370] [GTR parameters     ]
. (   33 sec) [    -20449.2367] [Alpha              ][  0.341329]
. (   34 sec) [    -20449.2282] [Branch lengths     ]
. (   35 sec) [    -20449.2282] [GTR parameters     ]
. (   36 sec) [    -20449.2282] [Alpha              ][  0.341329]
. (   38 sec) [    -20449.2250] [Branch lengths     ]
. (   39 sec) [    -20449.2250] [GTR parameters     ]
. (   39 sec) [    -20449.2250] [Alpha              ][  0.341329]
. (   41 sec) [    -20449.2230] [Branch lengths     ]
. (   42 sec) [    -20449.2230] [GTR parameters     ]
. (   42 sec) [    -20449.2230] [Alpha              ][  0.341329]
. (   44 sec) [    -20449.2214] [Branch lengths     ]
. (   45 sec) [    -20449.2214] [GTR parameters     ]
. (   45 sec) [    -20449.2214] [Alpha              ][  0.341329]
. (   47 sec) [    -20449.2198] [Branch lengths     ]
. (   48 sec) [    -20449.2198] [GTR parameters     ]
. (   48 sec) [    -20449.2198] [Alpha              ][  0.341329]
. (   50 sec) [    -20449.2182] [Branch lengths     ]
. (   51 sec) [    -20449.2182] [GTR parameters     ]
. (   51 sec) [    -20449.2182] [Alpha              ][  0.341329]
. (   53 sec) [    -20449.2167] [Branch lengths     ]
. (   54 sec) [    -20449.2167] [GTR parameters     ]
. (   55 sec) [    -20449.2167] [Alpha              ][  0.341329]
. (   56 sec) [    -20449.2152] [Branch lengths     ]
. (   57 sec) [    -20449.2152] [GTR parameters     ]
. (   58 sec) [    -20449.2152] [Alpha              ][  0.341329]
. (   59 sec) [    -20449.2137] [Branch lengths     ]
. (   60 sec) [    -20449.2137] [GTR parameters     ]
. (   61 sec) [    -20449.2137] [Alpha              ][  0.341329]
. (   63 sec) [    -20449.2122] [Branch lengths     ]
. (   64 sec) [    -20449.2122] [GTR parameters     ]
. (   64 sec) [    -20449.2122] [Alpha              ][  0.341329]
. (   66 sec) [    -20449.2107] [Branch lengths     ]
. (   67 sec) [    -20449.2107] [GTR parameters     ]
. (   67 sec) [    -20449.2107] [Alpha              ][  0.341329]
. (   69 sec) [    -20449.2091] [Branch lengths     ]
. (   70 sec) [    -20449.2091] [GTR parameters     ]
. (   70 sec) [    -20449.2091] [Alpha              ][  0.341329]
. (   72 sec) [    -20449.2075] [Branch lengths     ]
. (   73 sec) [    -20449.2075] [GTR parameters     ]
. (   73 sec) [    -20449.2075] [Alpha              ][  0.341329]
. (   75 sec) [    -20449.2072] [Branch lengths     ]
. (   76 sec) [    -20449.2072] [GTR parameters     ]
. (   77 sec) [    -20449.2072] [Alpha              ][  0.341329]
. (   81 sec) [    -20449.2072] [GTR parameters     ]
. (   81 sec) [    -20449.2072] [Alpha              ][  0.341329]
. Log likelihood of the current tree: -20449.207243.

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

. Printing the most likely tree in file 'nucleic_M2564_142x1130_2006.phy_phyml_tree.txt'...


. Time used 0h2m5s

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)