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

                . Sequence filename : 				 nucleic_M2587_117x1910_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_M2587_117x1910_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 1192 patterns found. (out of a total of 1910 sites) 

. 932 sites without polymorphism (48.80%).

. Reading tree...

. This analysis requires at least 74Mo of memory space.

. (    3 sec) [    -16509.3569] [Branch lengths     ]
. (   13 sec) [    -16161.2827] [GTR parameters     ]
. (   14 sec) [    -16009.0115] [Alpha              ][  0.500960]
. (   16 sec) [    -15998.1574] [Branch lengths     ]
. (   21 sec) [    -15997.9765] [GTR parameters     ]
. (   21 sec) [    -15989.5995] [Alpha              ][  0.413822]
. (   23 sec) [    -15984.0139] [Branch lengths     ]
. (   28 sec) [    -15983.9736] [GTR parameters     ]
. (   29 sec) [    -15983.4357] [Alpha              ][  0.394881]
. (   31 sec) [    -15979.6616] [Branch lengths     ]
. (   36 sec) [    -15979.6548] [GTR parameters     ]
. (   36 sec) [    -15979.3095] [Alpha              ][  0.380636]
. (   39 sec) [    -15977.2355] [Branch lengths     ]
. (   43 sec) [    -15977.2317] [GTR parameters     ]
. (   44 sec) [    -15977.0540] [Alpha              ][  0.370962]
. (   46 sec) [    -15975.9631] [Branch lengths     ]
. (   50 sec) [    -15975.9614] [GTR parameters     ]
. (   50 sec) [    -15975.8708] [Alpha              ][  0.364002]
. (   53 sec) [    -15975.2832] [Branch lengths     ]
. (   57 sec) [    -15975.2820] [GTR parameters     ]
. (   58 sec) [    -15975.2404] [Alpha              ][  0.359386]
. (   60 sec) [    -15974.9265] [Branch lengths     ]
. (   63 sec) [    -15974.9259] [GTR parameters     ]
. (   64 sec) [    -15974.9043] [Alpha              ][  0.356107]
. (   66 sec) [    -15974.7361] [Branch lengths     ]
. (   69 sec) [    -15974.7358] [GTR parameters     ]
. (   70 sec) [    -15974.7246] [Alpha              ][  0.353772]
. (   72 sec) [    -15974.6339] [Branch lengths     ]
. (   73 sec) [    -15974.6338] [GTR parameters     ]
. (   74 sec) [    -15974.6280] [Alpha              ][  0.352098]
. (   76 sec) [    -15974.5787] [Branch lengths     ]
. (   77 sec) [    -15974.5787] [GTR parameters     ]
. (   78 sec) [    -15974.5757] [Alpha              ][  0.350902]
. (   80 sec) [    -15974.5487] [Branch lengths     ]
. (   82 sec) [    -15974.5487] [GTR parameters     ]
. (   82 sec) [    -15974.5470] [Alpha              ][  0.349995]
. (   84 sec) [    -15974.5319] [Branch lengths     ]
. (   86 sec) [    -15974.5319] [GTR parameters     ]
. (   86 sec) [    -15974.5310] [Alpha              ][  0.349353]
. (   88 sec) [    -15974.5227] [Branch lengths     ]
. (   90 sec) [    -15974.5226] [GTR parameters     ]
. (   90 sec) [    -15974.5222] [Alpha              ][  0.348870]
. (   92 sec) [    -15974.5175] [Branch lengths     ]
. (   94 sec) [    -15974.5175] [GTR parameters     ]
. (   94 sec) [    -15974.5172] [Alpha              ][  0.348515]
. (   96 sec) [    -15974.5146] [Branch lengths     ]
. (   98 sec) [    -15974.5146] [GTR parameters     ]
. (   98 sec) [    -15974.5145] [Alpha              ][  0.348166]
. (  100 sec) [    -15974.5128] [Branch lengths     ]
. (  101 sec) [    -15974.5128] [GTR parameters     ]
. (  102 sec) [    -15974.5128] [Alpha              ][  0.348166]
. (  104 sec) [    -15974.5121] [Branch lengths     ]
. (  105 sec) [    -15974.5121] [GTR parameters     ]
. (  106 sec) [    -15974.5120] [Alpha              ][  0.347818]
. (  107 sec) [    -15974.5120] [GTR parameters     ]
. (  108 sec) [    -15974.5120] [Alpha              ][  0.347818]
. Log likelihood of the current tree: -15974.511981.

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

. Printing the most likely tree in file 'nucleic_M2587_117x1910_2006.phy_phyml_tree.txt'...


. Time used 0h2m44s

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)