Mercurial > repos > stephenshank > hyphy_fel

comparison messages.log @ 1:bb04851a0da1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 74206c79038a0dbd29a5581bf66e08721a4dfda2-dirty
author stephenshank
date Thu, 17 Jan 2019 14:10:34 -0500
parents 7f0a4907e2e4
children
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0:7f0a4907e2e4 1:bb04851a0da1
1 1
2 Loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
2 Loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf 3 Loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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8 Loaded 'libv3/stats.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/stats.bf
9 Loaded 'libv3/tasks/ancestral.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/ancestral.bf
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15 Loaded '../models/model_functions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/model_functions.bf 10 Loaded '../models/model_functions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/model_functions.bf
16 Loaded 'DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf 11 Loaded 'DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
17 Loaded 'frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf 12 Loaded 'frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
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36 Loaded 'libv3/models/codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
37 Loaded '../tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
38 Loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
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44 Loaded 'libv3/tasks/mpi.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/mpi.bf 48 Already loaded 'libv3/tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
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54 Loaded 'modules/selection_lib.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
47 Loaded 'libv3/models/codon/BS_REL.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf 55 Loaded 'libv3/models/codon/BS_REL.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
48 Loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf 56 Already loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
49 Loaded '../tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
50 Loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
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52 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
53 Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
54 Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf 57 Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
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58 Loaded 'MG_REV.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf 61 Loaded 'MG_REV.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
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65 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf 68 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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67 Loaded 'modules/io_functions.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
68 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
69 Already loaded 'libv3/IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
70 Already loaded 'libv3/convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
71 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
72 Loaded 'modules/selection_lib.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
73 Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used 70 Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used
74 Loaded 'modules/shared-load-file.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf 71 Loaded 'modules/shared-load-file.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
75 Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used 72 Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used
76 Already loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf 73 Already loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
77 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf 74 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
78 Variable 'bRvPSZrO.skipCodeSelectionStep' was not initialized prior to being used 75 Variable 'OWzuGPhH.skipCodeSelectionStep' was not initialized prior to being used
79 HyPhy killed by signal 2 76 Row and/or column partition is empty. All the data will be used by default.
77 Variable 'NEXUS_FILE_TREE_MATRIX' was not initialized prior to being used
78 Variable 'utility.ToggleEnvVariable.cache' was not initialized prior to being used
79 Variable 'TREE_NODE_NAME_MAPPING' was not initialized prior to being used
80 Variable 'Gibbjnoz.PROMPT_FOR_FILE' was not initialized prior to being used
81 Variable 'END_OF_FILE' was not initialized prior to being used
82 Variable '_DO_TREE_REBALANCE_' was not initialized prior to being used
83 Variable '_KEEP_I_LABELS_' was not initialized prior to being used
84 Variable 'INCLUDE_MODEL_SPECS' was not initialized prior to being used
85 Variable 'utility.ForEachPair.warn_non_rentrant' was not initialized prior to being used
86 Row and/or column partition is empty. All the data will be used by default.
87 Row and/or column partition is empty. All the data will be used by default.
88 Variable 'zpqXEbDu.cache' was not initialized prior to being used
89 Row and/or column partition is empty. All the data will be used by default.
90 Variable 'COUNT_GAPS_IN_FREQUENCIES' was not initialized prior to being used
91 Variable 'NRSKiVtk.model_pi' was not initialized prior to being used
92 Model NRSKiVtk.model assigned to Pig
93 Model NRSKiVtk.model assigned to Cow
94 Model NRSKiVtk.model assigned to Node3
95 Model NRSKiVtk.model assigned to Horse
96 Model NRSKiVtk.model assigned to Cat
97 Model NRSKiVtk.model assigned to Node2
98 Model NRSKiVtk.model assigned to RhMonkey
99 Model NRSKiVtk.model assigned to Baboon
100 Model NRSKiVtk.model assigned to Node9
101 Model NRSKiVtk.model assigned to Human
102 Model NRSKiVtk.model assigned to Chimp
103 Model NRSKiVtk.model assigned to Node12
104 Model NRSKiVtk.model assigned to Node8
105 Model NRSKiVtk.model assigned to Node1
106 Model NRSKiVtk.model assigned to Rat
107 Model NRSKiVtk.model assigned to Mouse
108 The tips of the tree:NRSKiVtk.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
109
110 Pseudo-optimal path's cost 2330 vs 4284 for 1..k=> a 1.83863 x improvement
111 Partition 0 reversible model flag computed as 1
112 Variable 'USE_LAST_RESULTS' was not initialized prior to being used
113 Variable 'NRSKiVtk.tree_0.Pig.t' was not initialized prior to being used
114 models.generic.SetBranchLength: NRSKiVtk.tree_0.Pig.t=0.3974535884114245
115 Variable 'NRSKiVtk.tree_0.Cow.t' was not initialized prior to being used
116 models.generic.SetBranchLength: NRSKiVtk.tree_0.Cow.t=0.5732857515739808
117 Variable 'NRSKiVtk.tree_0.Node3.t' was not initialized prior to being used
118 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node3.t=0.2285810062933711
119 Variable 'NRSKiVtk.tree_0.Horse.t' was not initialized prior to being used
120 models.generic.SetBranchLength: NRSKiVtk.tree_0.Horse.t=0.445313802634098
121 Variable 'NRSKiVtk.tree_0.Cat.t' was not initialized prior to being used
122 models.generic.SetBranchLength: NRSKiVtk.tree_0.Cat.t=0.7112847618952328
123 Variable 'NRSKiVtk.tree_0.Node2.t' was not initialized prior to being used
124 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node2.t=0.1574326532610344
125 Variable 'NRSKiVtk.tree_0.RhMonkey.t' was not initialized prior to being used
126 models.generic.SetBranchLength: NRSKiVtk.tree_0.RhMonkey.t=0.00541241057687097
127 Variable 'NRSKiVtk.tree_0.Baboon.t' was not initialized prior to being used
128 models.generic.SetBranchLength: NRSKiVtk.tree_0.Baboon.t=0.008348273981595522
129 Variable 'NRSKiVtk.tree_0.Node9.t' was not initialized prior to being used
130 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node9.t=0.06106219833449517
131 Variable 'NRSKiVtk.tree_0.Human.t' was not initialized prior to being used
132 models.generic.SetBranchLength: NRSKiVtk.tree_0.Human.t=0.01168167424258652
133 Variable 'NRSKiVtk.tree_0.Chimp.t' was not initialized prior to being used
134 models.generic.SetBranchLength: NRSKiVtk.tree_0.Chimp.t=0.00214616181187092
135 Variable 'NRSKiVtk.tree_0.Node12.t' was not initialized prior to being used
136 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node12.t=0.03189158847602433
137 Variable 'NRSKiVtk.tree_0.Node8.t' was not initialized prior to being used
138 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node8.t=0.2735913110261884
139 Variable 'NRSKiVtk.tree_0.Node1.t' was not initialized prior to being used
140 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node1.t=0.9154145654683773
141 Variable 'NRSKiVtk.tree_0.Rat.t' was not initialized prior to being used
142 models.generic.SetBranchLength: NRSKiVtk.tree_0.Rat.t=0.1368762373082833
143 Variable 'NRSKiVtk.tree_0.Mouse.t' was not initialized prior to being used
144 models.generic.SetBranchLength: NRSKiVtk.tree_0.Mouse.t=0.2630995612925615
145 Variable 'NRSKiVtk.NRSKiVtk.likelihoodFunction' was not initialized prior to being used
146 Variable 'SAVE_OPT_STATUS_TO' was not initialized prior to being used
147 Set GUI update interval to every 357-th LF evaluation.
148 Optimization settings:
149 OPTIMIZATION_METHOD = 4
150 OPTIMIZATION_PRECISION = 0.001
151 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
152
153 Initial parameter values
154
155 NRSKiVtk.model.theta_GT = 0.25
156 NRSKiVtk.model.theta_CG = 0.25
157 NRSKiVtk.model.theta_CT = 1
158 NRSKiVtk.model.theta_AT = 0.25
159 NRSKiVtk.model.theta_AC = 0.25
160 NRSKiVtk.tree_0.Pig.t = 0.397454
161 NRSKiVtk.tree_0.Cow.t = 0.573286
162 NRSKiVtk.tree_0.Node3.t = 0.228581
163 NRSKiVtk.tree_0.Horse.t = 0.445314
164 NRSKiVtk.tree_0.Cat.t = 0.711285
165 NRSKiVtk.tree_0.Node2.t = 0.157433
166 NRSKiVtk.tree_0.RhMonkey.t = 0.00541241
167 NRSKiVtk.tree_0.Baboon.t = 0.00834827
168 NRSKiVtk.tree_0.Node9.t = 0.0610622
169 NRSKiVtk.tree_0.Human.t = 0.0116817
170 NRSKiVtk.tree_0.Chimp.t = 0.00214616
171 NRSKiVtk.tree_0.Node12.t = 0.0318916
172 NRSKiVtk.tree_0.Node8.t = 0.273591
173 NRSKiVtk.tree_0.Node1.t = 0.915415
174 NRSKiVtk.tree_0.Rat.t = 0.136876
175 NRSKiVtk.tree_0.Mouse.t = 0.2631
176 Optimization finished in 25 loop passes.
177 1667 likelihood evaluation calls and 12169 matrix exponentiations calls were made
178
179 Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used
180 Variable 'NRSKiVtk.option' was not initialized prior to being used
181 Variable 'busted.terms.json.nucleotide_gtr' was not initialized prior to being used
182 Variable 'Unknown' was not initialized prior to being used
183 Variable 'ThTEDPSn.initial_value' was not initialized prior to being used
184 Variable 'dIONygHy.data_filter' was not initialized prior to being used
185 Row and/or column partition is empty. All the data will be used by default.
186 Set GUI update interval to every 2834-th LF evaluation.
187 Optimization settings:
188 OPTIMIZATION_METHOD = 4
189 OPTIMIZATION_PRECISION = 0.001
190 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
191
192 Initial parameter values
193
194 frequencies._aux.CF3x4.p0_0 = 0.415775
195 frequencies._aux.CF3x4.p0_1 = 0.250343
196 frequencies._aux.CF3x4.p0_2 = 0.652625
197 frequencies._aux.CF3x4.p1_0 = 0.399465
198 frequencies._aux.CF3x4.p1_1 = 0.28317
199 frequencies._aux.CF3x4.p1_2 = 0.391304
200 frequencies._aux.CF3x4.p2_0 = 0.253743
201 frequencies._aux.CF3x4.p2_1 = 0.314941
202 frequencies._aux.CF3x4.p2_2 = 0.521444
203 Optimization finished in 5 loop passes.
204 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
205
206 Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
207 Model dIONygHy.model_MGREV assigned to Pig
208 Model dIONygHy.model_MGREV assigned to Cow
209 Model dIONygHy.model_MGREV assigned to Node3
210 Model dIONygHy.model_MGREV assigned to Horse
211 Model dIONygHy.model_MGREV assigned to Cat
212 Model dIONygHy.model_MGREV assigned to Node2
213 Model dIONygHy.model_MGREV assigned to RhMonkey
214 Model dIONygHy.model_MGREV assigned to Baboon
215 Model dIONygHy.model_MGREV assigned to Node9
216 Model dIONygHy.model_MGREV assigned to Human
217 Model dIONygHy.model_MGREV assigned to Chimp
218 Model dIONygHy.model_MGREV assigned to Node12
219 Model dIONygHy.model_MGREV assigned to Node8
220 Model dIONygHy.model_MGREV assigned to Node1
221 Model dIONygHy.model_MGREV assigned to Rat
222 Model dIONygHy.model_MGREV assigned to Mouse
223 The tips of the tree:dIONygHy.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
224
225 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
226 Partition 0 reversible model flag computed as 1
227 Variable 'dIONygHy.dIONygHy.likelihoodFunction' was not initialized prior to being used
228 Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
229 Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
230 Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
231 Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
232 Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
233 Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
234 Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
235 Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
236 Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
237 Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
238 Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
239 Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
240 Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
241 Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
242 Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
243 Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
244 Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
245 Set GUI update interval to every 208-th LF evaluation.
246 Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
247 Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
248 Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
249 Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
250 Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
251 Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
252 Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
253 Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
254 Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
255 Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
256 Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
257 Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
258 Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
259 Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
260 Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
261 Optimization settings:
262 OPTIMIZATION_METHOD = 4
263 OPTIMIZATION_PRECISION = 0.001
264 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
265
266 Initial parameter values
267
268 dIONygHy.model_MGREV.theta_CT = 1
269 dIONygHy.model_MGREV.theta_GT = 1
270 dIONygHy.model_MGREV.theta_CG = 1
271 dIONygHy.model_MGREV.theta_AC = 1
272 dIONygHy.model_MGREV.theta_AT = 1
273 dIONygHy.model_MGREV.omega_0 = 1
274 dIONygHy.tree_0.Pig.alpha = 0.000173063
275 dIONygHy.tree_0.Cow.alpha = 0.000186779
276 dIONygHy.tree_0.Node3.alpha = 1.15458e-05
277 dIONygHy.tree_0.Horse.alpha = 0.000174488
278 dIONygHy.tree_0.Cat.alpha = 0.000196799
279 dIONygHy.tree_0.Node2.alpha = 0.000173618
280 dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
281 dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
282 dIONygHy.tree_0.Node9.alpha = 0.000140119
283 dIONygHy.tree_0.Human.alpha = 7.93383e-07
284 dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
285 dIONygHy.tree_0.Node12.alpha = 2.75759e-05
286 dIONygHy.tree_0.Node8.alpha = 4.67029e-05
287 dIONygHy.tree_0.Node1.alpha = 0.1
288 dIONygHy.tree_0.Rat.alpha = 8.26646e-05
289 dIONygHy.tree_0.Mouse.alpha = 0.000107933
290 Optimization finished in 35 loop passes.
291 3927 likelihood evaluation calls and 23083 matrix exponentiations calls were made
292
293 Row and/or column partition is empty. All the data will be used by default.
294 Set GUI update interval to every 2909-th LF evaluation.
295 Optimization settings:
296 OPTIMIZATION_METHOD = 4
297 OPTIMIZATION_PRECISION = 0.001
298 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
299
300 Initial parameter values
301
302 frequencies._aux.CF3x4.p0_0 = 0.415775
303 frequencies._aux.CF3x4.p0_1 = 0.250343
304 frequencies._aux.CF3x4.p0_2 = 0.652625
305 frequencies._aux.CF3x4.p1_0 = 0.399465
306 frequencies._aux.CF3x4.p1_1 = 0.28317
307 frequencies._aux.CF3x4.p1_2 = 0.391304
308 frequencies._aux.CF3x4.p2_0 = 0.253743
309 frequencies._aux.CF3x4.p2_1 = 0.314941
310 frequencies._aux.CF3x4.p2_2 = 0.521444
311 Optimization finished in 5 loop passes.
312 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
313
314 Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
315 Model dIONygHy.model_MGREV assigned to Pig
316 Model dIONygHy.model_MGREV assigned to Cow
317 Model dIONygHy.model_MGREV assigned to Node3
318 Model dIONygHy.model_MGREV assigned to Horse
319 Model dIONygHy.model_MGREV assigned to Cat
320 Model dIONygHy.model_MGREV assigned to Node2
321 Model dIONygHy.model_MGREV assigned to RhMonkey
322 Model dIONygHy.model_MGREV assigned to Baboon
323 Model dIONygHy.model_MGREV assigned to Node9
324 Model dIONygHy.model_MGREV assigned to Human
325 Model dIONygHy.model_MGREV assigned to Chimp
326 Model dIONygHy.model_MGREV assigned to Node12
327 Model dIONygHy.model_MGREV assigned to Node8
328 Model dIONygHy.model_MGREV assigned to Node1
329 Model dIONygHy.model_MGREV assigned to Rat
330 Model dIONygHy.model_MGREV assigned to Mouse
331 The tips of the tree:dIONygHy.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
332
333 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
334 Partition 0 reversible model flag computed as 1
335 Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
336 Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
337 Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
338 Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
339 Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
340 Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
341 Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
342 Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
343 Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
344 Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
345 Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
346 Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
347 Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
348 Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
349 Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
350 Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
351 Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
352 Set GUI update interval to every 269-th LF evaluation.
353 Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
354 Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
355 Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
356 Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
357 Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
358 Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
359 Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
360 Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
361 Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
362 Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
363 Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
364 Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
365 Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
366 Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
367 Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
368 Optimization settings:
369 OPTIMIZATION_METHOD = 4
370 OPTIMIZATION_PRECISION = 0.001
371 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
372
373 Initial parameter values
374
375 dIONygHy.model_MGREV.theta_CG = 1
376 dIONygHy.model_MGREV.theta_AT = 1
377 dIONygHy.model_MGREV.theta_CT = 1
378 dIONygHy.model_MGREV.theta_GT = 1
379 dIONygHy.model_MGREV.theta_AC = 1
380 dIONygHy.model_MGREV.omega_0 = 1
381 dIONygHy.tree_0.Pig.alpha = 0.000173063
382 dIONygHy.tree_0.Cow.alpha = 0.000186779
383 dIONygHy.tree_0.Node3.alpha = 1.15458e-05
384 dIONygHy.tree_0.Horse.alpha = 0.000174488
385 dIONygHy.tree_0.Cat.alpha = 0.000196799
386 dIONygHy.tree_0.Node2.alpha = 0.000173618
387 dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
388 dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
389 dIONygHy.tree_0.Node9.alpha = 0.000140119
390 dIONygHy.tree_0.Human.alpha = 7.93383e-07
391 dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
392 dIONygHy.tree_0.Node12.alpha = 2.75759e-05
393 dIONygHy.tree_0.Node8.alpha = 4.67029e-05
394 dIONygHy.tree_0.Node1.alpha = 0.1
395 dIONygHy.tree_0.Rat.alpha = 8.26646e-05
396 dIONygHy.tree_0.Mouse.alpha = 0.000107933
397 Optimization finished in 35 loop passes.
398 3276 likelihood evaluation calls and 21044 matrix exponentiations calls were made
399
400 Overwritten previously defined function:'IIsiGihg.rate_generator'
401 Overwritten previously defined function:'IIsiGihg.rate_generator'
402 Set GUI update interval to every 3023-th LF evaluation.
403 Optimization settings:
404 OPTIMIZATION_METHOD = 4
405 OPTIMIZATION_PRECISION = 0.001
406 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
407
408 Initial parameter values
409
410 frequencies._aux.CF3x4.p0_0 = 0.415775
411 frequencies._aux.CF3x4.p0_1 = 0.250343
412 frequencies._aux.CF3x4.p0_2 = 0.652625
413 frequencies._aux.CF3x4.p1_0 = 0.399465
414 frequencies._aux.CF3x4.p1_1 = 0.28317
415 frequencies._aux.CF3x4.p1_2 = 0.391304
416 frequencies._aux.CF3x4.p2_0 = 0.253743
417 frequencies._aux.CF3x4.p2_1 = 0.314941
418 frequencies._aux.CF3x4.p2_2 = 0.521444
419 Optimization finished in 5 loop passes.
420 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
421
422 Variable 'busted.test_pi' was not initialized prior to being used
423 Overwritten previously defined function:'IIsiGihg.rate_generator'
424 Overwritten previously defined function:'IIsiGihg.rate_generator'
425 Overwritten previously defined function:'IIsiGihg.rate_generator'
426 Set GUI update interval to every 3010-th LF evaluation.
427 Optimization settings:
428 OPTIMIZATION_METHOD = 4
429 OPTIMIZATION_PRECISION = 0.001
430 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
431
432 Initial parameter values
433
434 frequencies._aux.CF3x4.p0_0 = 0.415775
435 frequencies._aux.CF3x4.p0_1 = 0.250343
436 frequencies._aux.CF3x4.p0_2 = 0.652625
437 frequencies._aux.CF3x4.p1_0 = 0.399465
438 frequencies._aux.CF3x4.p1_1 = 0.28317
439 frequencies._aux.CF3x4.p1_2 = 0.391304
440 frequencies._aux.CF3x4.p2_0 = 0.253743
441 frequencies._aux.CF3x4.p2_1 = 0.314941
442 frequencies._aux.CF3x4.p2_2 = 0.521444
443 Optimization finished in 5 loop passes.
444 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
445
446 Variable 'busted.background_pi' was not initialized prior to being used
447 Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used
448 No nodel was assigned to Pig
449 No nodel was assigned to Cow
450 No nodel was assigned to Node3
451 No nodel was assigned to Horse
452 No nodel was assigned to Cat
453 No nodel was assigned to Node2
454 No nodel was assigned to RhMonkey
455 No nodel was assigned to Baboon
456 No nodel was assigned to Node9
457 No nodel was assigned to Human
458 No nodel was assigned to Chimp
459 No nodel was assigned to Node12
460 No nodel was assigned to Node8
461 No nodel was assigned to Node1
462 No nodel was assigned to Rat
463 No nodel was assigned to Mouse
464 The tips of the tree:CPXgZuSs.tree_id_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
465
466 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
467 Partition 0 is ASSUMED to have a reversible model
468 busted.test.theta_AG was already constrained in estimators.SetGlobals2
469 Variable 'CPXgZuSs.tree_id_0.Pig.t' was not initialized prior to being used
470 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Pig.t=1.377886710534728
471 Variable 'CPXgZuSs.tree_id_0.Cow.t' was not initialized prior to being used
472 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cow.t=1.774251775766245
473 Variable 'CPXgZuSs.tree_id_0.Node3.t' was not initialized prior to being used
474 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node3.t=0.727900992785442
475 Variable 'CPXgZuSs.tree_id_0.Horse.t' was not initialized prior to being used
476 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Horse.t=1.51058601207266
477 Variable 'CPXgZuSs.tree_id_0.Cat.t' was not initialized prior to being used
478 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cat.t=1.957296993203762
479 Variable 'CPXgZuSs.tree_id_0.Node2.t' was not initialized prior to being used
480 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node2.t=0.4612561973173576
481 Variable 'CPXgZuSs.tree_id_0.RhMonkey.t' was not initialized prior to being used
482 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.RhMonkey.t=0.02659579655381833
483 Variable 'CPXgZuSs.tree_id_0.Baboon.t' was not initialized prior to being used
484 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Baboon.t=0.01267390527294645
485 Variable 'CPXgZuSs.tree_id_0.Node9.t' was not initialized prior to being used
486 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node9.t=0.1855677984720407
487 Variable 'CPXgZuSs.tree_id_0.Human.t' was not initialized prior to being used
488 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Human.t=0
489 Variable 'CPXgZuSs.tree_id_0.Chimp.t' was not initialized prior to being used
490 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Chimp.t=0.01307822802283968
491 Variable 'CPXgZuSs.tree_id_0.Node12.t' was not initialized prior to being used
492 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node12.t=0.1279673910082466
493 Variable 'CPXgZuSs.tree_id_0.Node8.t' was not initialized prior to being used
494 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node8.t=0.7824909790907859
495 Variable 'CPXgZuSs.tree_id_0.Node1.t' was not initialized prior to being used
496 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node1.t=2.034207610785829
497 Variable 'CPXgZuSs.tree_id_0.Rat.t' was not initialized prior to being used
498 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Rat.t=0.4799151894651191
499 Variable 'CPXgZuSs.tree_id_0.Mouse.t' was not initialized prior to being used
500 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Mouse.t=0.859781481367942
501 Variable 'CPXgZuSs.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
502 Set GUI update interval to every 17-th LF evaluation.
503 Optimization settings:
504 OPTIMIZATION_METHOD = 4
505 OPTIMIZATION_PRECISION = 0.001
506 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
507
508 Initial parameter values
509
510 busted.test.theta_AC = 0.575889
511 busted.test.theta_AT = 0.266515
512 busted.test.omega1 = 0
513 busted.test.bsrel_mixture_aux_0 = 0.7
514 busted.test.theta_CG = 0.470944
515 busted.test.omega3 = 9.52381
516 busted.test.omega2 = 0.238095
517 busted.test.theta_CT = 0.973284
518 busted.test.bsrel_mixture_aux_1 = 0.666667
519 busted.test.theta_GT = 0.315964
520 CPXgZuSs.tree_id_0.Pig.t = 1.37789
521 CPXgZuSs.tree_id_0.Cow.t = 1.77425
522 CPXgZuSs.tree_id_0.Node3.t = 0.727901
523 CPXgZuSs.tree_id_0.Horse.t = 1.51059
524 CPXgZuSs.tree_id_0.Cat.t = 1.9573
525 CPXgZuSs.tree_id_0.Node2.t = 0.461256
526 CPXgZuSs.tree_id_0.RhMonkey.t = 0.0265958
527 CPXgZuSs.tree_id_0.Baboon.t = 0.0126739
528 CPXgZuSs.tree_id_0.Node9.t = 0.185568
529 CPXgZuSs.tree_id_0.Human.t = 0
530 CPXgZuSs.tree_id_0.Chimp.t = 0.0130782
531 CPXgZuSs.tree_id_0.Node12.t = 0.127967
532 CPXgZuSs.tree_id_0.Node8.t = 0.782491
533 CPXgZuSs.tree_id_0.Node1.t = 2.03421
534 CPXgZuSs.tree_id_0.Rat.t = 0.479915
535 CPXgZuSs.tree_id_0.Mouse.t = 0.859781
536 Optimization finished in 26 loop passes.
537 2990 likelihood evaluation calls and 70968 matrix exponentiations calls were made
538
539 Variable 'KIGDLXKi.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
540 Set GUI update interval to every 28-th LF evaluation.
541 Optimization settings:
542 OPTIMIZATION_METHOD = 4
543 OPTIMIZATION_PRECISION = 0.001
544 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
545
546 Initial parameter values
547
548 busted.test.theta_AC = 0.468589
549 busted.test.omega1 = 0.210733
550 busted.test.bsrel_mixture_aux_0 = 0.412135
551 busted.test.theta_AT = 0.215633
552 busted.test.omega2 = 0.105287
553 busted.test.bsrel_mixture_aux_1 = 0.404693
554 busted.test.theta_CT = 0.973171
555 busted.test.theta_GT = 0.273282
556 busted.test.theta_CG = 0.415669
557 CPXgZuSs.tree_id_0.Pig.t = 0.410826
558 CPXgZuSs.tree_id_0.Cow.t = 0.555921
559 CPXgZuSs.tree_id_0.Node3.t = 0.241332
560 CPXgZuSs.tree_id_0.Horse.t = 0.483056
561 CPXgZuSs.tree_id_0.Cat.t = 0.61829
562 CPXgZuSs.tree_id_0.Node2.t = 0.117184
563 CPXgZuSs.tree_id_0.RhMonkey.t = 0.00689772
564 CPXgZuSs.tree_id_0.Baboon.t = 0.0034792
565 CPXgZuSs.tree_id_0.Node9.t = 0.051855
566 CPXgZuSs.tree_id_0.Human.t = 0
567 CPXgZuSs.tree_id_0.Chimp.t = 0.00344635
568 CPXgZuSs.tree_id_0.Node12.t = 0.0343399
569 CPXgZuSs.tree_id_0.Node8.t = 0.253166
570 CPXgZuSs.tree_id_0.Node1.t = 0.86218
571 CPXgZuSs.tree_id_0.Rat.t = 0.138343
572 CPXgZuSs.tree_id_0.Mouse.t = 0.279774
573 Optimization finished in 14 loop passes.
574 1338 likelihood evaluation calls and 35802 matrix exponentiations calls were made
575
576 Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used