..........................                                      
 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 (RAxML_result.nucleic_M2627_54x1915_2006.phy_RAXML_CAT)"
                . 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) [    -37322.8929] [Branch lengths     ]
. (    3 sec) [    -36393.2170] [GTR parameters     ]
. (    3 sec) [    -36263.5489] [Alpha              ][  0.601046]
. (    5 sec) [    -36243.3074] [Branch lengths     ]
. (   12 sec) [    -35295.4963] [GTR parameters     ]
. (   12 sec) [    -35280.2514] [Alpha              ][  0.505431]
. (   14 sec) [    -35265.4436] [Branch lengths     ]
. (   21 sec) [    -35262.3541] [GTR parameters     ]
. (   21 sec) [    -35262.1774] [Alpha              ][  0.496442]
. (   22 sec) [    -35258.2168] [Branch lengths     ]
. (   25 sec) [    -35257.9045] [GTR parameters     ]
. (   26 sec) [    -35257.9018] [Alpha              ][  0.497531]
. (   27 sec) [    -35255.9457] [Branch lengths     ]
. (   31 sec) [    -35255.8394] [GTR parameters     ]
. (   32 sec) [    -35255.8334] [Alpha              ][  0.499189]
. (   33 sec) [    -35254.8067] [Branch lengths     ]
. (   34 sec) [    -35254.7582] [GTR parameters     ]
. (   34 sec) [    -35254.7579] [Alpha              ][  0.499688]
. (   35 sec) [    -35254.1354] [Branch lengths     ]
. (   37 sec) [    -35254.1034] [GTR parameters     ]
. (   37 sec) [    -35254.1033] [Alpha              ][  0.500188]
. (   38 sec) [    -35253.7542] [Branch lengths     ]
. (   39 sec) [    -35253.7366] [GTR parameters     ]
. (   39 sec) [    -35253.7364] [Alpha              ][  0.499687]
. (   41 sec) [    -35253.5135] [Branch lengths     ]
. (   42 sec) [    -35253.5012] [GTR parameters     ]
. (   42 sec) [    -35253.5012] [Alpha              ][  0.499687]
. (   43 sec) [    -35253.3727] [Branch lengths     ]
. (   44 sec) [    -35253.3652] [GTR parameters     ]
. (   44 sec) [    -35253.3652] [Alpha              ][  0.499687]
. (   45 sec) [    -35253.2793] [Branch lengths     ]
. (   46 sec) [    -35253.2749] [GTR parameters     ]
. (   46 sec) [    -35253.2749] [Alpha              ][  0.499687]
. (   48 sec) [    -35253.2232] [Branch lengths     ]
. (   48 sec) [    -35253.2209] [GTR parameters     ]
. (   49 sec) [    -35253.2209] [Alpha              ][  0.499687]
. (   50 sec) [    -35253.1867] [Branch lengths     ]
. (   50 sec) [    -35253.1852] [GTR parameters     ]
. (   51 sec) [    -35253.1852] [Alpha              ][  0.499687]
. (   52 sec) [    -35253.1659] [Branch lengths     ]
. (   53 sec) [    -35253.1642] [GTR parameters     ]
. (   53 sec) [    -35253.1639] [Alpha              ][  0.499188]
. (   54 sec) [    -35253.1503] [Branch lengths     ]
. (   55 sec) [    -35253.1492] [GTR parameters     ]
. (   55 sec) [    -35253.1492] [Alpha              ][  0.499188]
. (   56 sec) [    -35253.1406] [Branch lengths     ]
. (   57 sec) [    -35253.1402] [GTR parameters     ]
. (   57 sec) [    -35253.1402] [Alpha              ][  0.499188]
. (   58 sec) [    -35253.1343] [Branch lengths     ]
. (   60 sec) [    -35253.1340] [GTR parameters     ]
. (   60 sec) [    -35253.1340] [Alpha              ][  0.499188]
. (   61 sec) [    -35253.1305] [Branch lengths     ]
. (   62 sec) [    -35253.1303] [GTR parameters     ]
. (   62 sec) [    -35253.1303] [Alpha              ][  0.499188]
. (   63 sec) [    -35253.1279] [Branch lengths     ]
. (   64 sec) [    -35253.1278] [GTR parameters     ]
. (   64 sec) [    -35253.1278] [Alpha              ][  0.499188]
. (   65 sec) [    -35253.1264] [Branch lengths     ]
. (   66 sec) [    -35253.1264] [GTR parameters     ]
. (   66 sec) [    -35253.1264] [Alpha              ][  0.499188]
. (   67 sec) [    -35253.1255] [Branch lengths     ]
. (   68 sec) [    -35253.1254] [GTR parameters     ]
. (   68 sec) [    -35253.1254] [Alpha              ][  0.499188]
. (   69 sec) [    -35253.1254] [GTR parameters     ]
. (   69 sec) [    -35253.1254] [Alpha              ][  0.499188]
. Log likelihood of the current tree: -35253.125418.

. 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 0h1m38s

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)