Mercurial > repos > stephenshank > hyphy_fel


Loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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Loaded 'libv3/tasks/estimators.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/estimators.bf
Loaded '../models/model_functions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/model_functions.bf
Loaded 'DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
Loaded 'frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
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Loaded 'parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
Loaded 'GrabBag' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/Utility/GrabBag.bf
Overwritten previously defined function:'_sortStringsAux'
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Loaded '../models/DNA/GTR.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA/GTR.bf
Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
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Loaded 'libv3/tasks/alignments.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/alignments.bf
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Loaded 'libv3/models/codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
Loaded '../tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
Loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'libv3/tasks/trees.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/trees.bf
Already loaded '../IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
Already loaded '../convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'TreeTools' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/TreeTools.ibf
Already loaded 'libv3/tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
Loaded 'modules/io_functions.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Already loaded 'libv3/IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
Already loaded 'libv3/convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'modules/selection_lib.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
Loaded 'libv3/models/codon/BS_REL.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
Already loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
Already loaded '../parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
Already loaded '../frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
Already loaded '../../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'MG_REV.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
Already loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
Already loaded '../parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
Already loaded '../frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
Already loaded '../../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded '../../convenience/math.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/math.bf
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Already loaded 'libv3/convenience/math.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/math.bf
Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used
Loaded 'modules/shared-load-file.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used
Already loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Variable 'OWzuGPhH.skipCodeSelectionStep' was not initialized prior to being used
Row and/or column partition is empty. All the data will be used by default.
Variable 'NEXUS_FILE_TREE_MATRIX' was not initialized prior to being used
Variable 'utility.ToggleEnvVariable.cache' was not initialized prior to being used
Variable 'TREE_NODE_NAME_MAPPING' was not initialized prior to being used
Variable 'Gibbjnoz.PROMPT_FOR_FILE' was not initialized prior to being used
Variable 'END_OF_FILE' was not initialized prior to being used
Variable '_DO_TREE_REBALANCE_' was not initialized prior to being used
Variable '_KEEP_I_LABELS_' was not initialized prior to being used
Variable 'INCLUDE_MODEL_SPECS' was not initialized prior to being used
Variable 'utility.ForEachPair.warn_non_rentrant' was not initialized prior to being used
Row and/or column partition is empty. All the data will be used by default.
Row and/or column partition is empty. All the data will be used by default.
Variable 'zpqXEbDu.cache' was not initialized prior to being used
Row and/or column partition is empty. All the data will be used by default.
Variable 'COUNT_GAPS_IN_FREQUENCIES' was not initialized prior to being used
Variable 'NRSKiVtk.model_pi' was not initialized prior to being used
Model NRSKiVtk.model assigned to Pig
Model NRSKiVtk.model assigned to Cow
Model NRSKiVtk.model assigned to Node3
Model NRSKiVtk.model assigned to Horse
Model NRSKiVtk.model assigned to Cat
Model NRSKiVtk.model assigned to Node2
Model NRSKiVtk.model assigned to RhMonkey
Model NRSKiVtk.model assigned to Baboon
Model NRSKiVtk.model assigned to Node9
Model NRSKiVtk.model assigned to Human
Model NRSKiVtk.model assigned to Chimp
Model NRSKiVtk.model assigned to Node12
Model NRSKiVtk.model assigned to Node8
Model NRSKiVtk.model assigned to Node1
Model NRSKiVtk.model assigned to Rat
Model NRSKiVtk.model assigned to Mouse
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}

Pseudo-optimal path's cost 2330 vs 4284 for 1..k=> a 1.83863 x improvement
Partition 0 reversible model flag computed as 1
Variable 'USE_LAST_RESULTS' was not initialized prior to being used
Variable 'NRSKiVtk.tree_0.Pig.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Pig.t=0.3974535884114245
Variable 'NRSKiVtk.tree_0.Cow.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Cow.t=0.5732857515739808
Variable 'NRSKiVtk.tree_0.Node3.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Node3.t=0.2285810062933711
Variable 'NRSKiVtk.tree_0.Horse.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Horse.t=0.445313802634098
Variable 'NRSKiVtk.tree_0.Cat.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Cat.t=0.7112847618952328
Variable 'NRSKiVtk.tree_0.Node2.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Node2.t=0.1574326532610344
Variable 'NRSKiVtk.tree_0.RhMonkey.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.RhMonkey.t=0.00541241057687097
Variable 'NRSKiVtk.tree_0.Baboon.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Baboon.t=0.008348273981595522
Variable 'NRSKiVtk.tree_0.Node9.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Node9.t=0.06106219833449517
Variable 'NRSKiVtk.tree_0.Human.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Human.t=0.01168167424258652
Variable 'NRSKiVtk.tree_0.Chimp.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Chimp.t=0.00214616181187092
Variable 'NRSKiVtk.tree_0.Node12.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Node12.t=0.03189158847602433
Variable 'NRSKiVtk.tree_0.Node8.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Node8.t=0.2735913110261884
Variable 'NRSKiVtk.tree_0.Node1.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Node1.t=0.9154145654683773
Variable 'NRSKiVtk.tree_0.Rat.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Rat.t=0.1368762373082833
Variable 'NRSKiVtk.tree_0.Mouse.t' was not initialized prior to being used
models.generic.SetBranchLength: NRSKiVtk.tree_0.Mouse.t=0.2630995612925615
Variable 'NRSKiVtk.NRSKiVtk.likelihoodFunction' was not initialized prior to being used
Variable 'SAVE_OPT_STATUS_TO' was not initialized prior to being used
Set GUI update interval to every 357-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

NRSKiVtk.model.theta_GT = 0.25
NRSKiVtk.model.theta_CG = 0.25
NRSKiVtk.model.theta_CT = 1
NRSKiVtk.model.theta_AT = 0.25
NRSKiVtk.model.theta_AC = 0.25
NRSKiVtk.tree_0.Pig.t = 0.397454
NRSKiVtk.tree_0.Cow.t = 0.573286
NRSKiVtk.tree_0.Node3.t = 0.228581
NRSKiVtk.tree_0.Horse.t = 0.445314
NRSKiVtk.tree_0.Cat.t = 0.711285
NRSKiVtk.tree_0.Node2.t = 0.157433
NRSKiVtk.tree_0.RhMonkey.t = 0.00541241
NRSKiVtk.tree_0.Baboon.t = 0.00834827
NRSKiVtk.tree_0.Node9.t = 0.0610622
NRSKiVtk.tree_0.Human.t = 0.0116817
NRSKiVtk.tree_0.Chimp.t = 0.00214616
NRSKiVtk.tree_0.Node12.t = 0.0318916
NRSKiVtk.tree_0.Node8.t = 0.273591
NRSKiVtk.tree_0.Node1.t = 0.915415
NRSKiVtk.tree_0.Rat.t = 0.136876
NRSKiVtk.tree_0.Mouse.t = 0.2631
Optimization finished in 25 loop passes.
1667 likelihood evaluation calls and 12169 matrix exponentiations calls were made

Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used
Variable 'NRSKiVtk.option' was not initialized prior to being used
Variable 'busted.terms.json.nucleotide_gtr' was not initialized prior to being used
Variable 'Unknown' was not initialized prior to being used
Variable 'ThTEDPSn.initial_value' was not initialized prior to being used
Variable 'dIONygHy.data_filter' was not initialized prior to being used
Row and/or column partition is empty. All the data will be used by default.
Set GUI update interval to every 2834-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

frequencies._aux.CF3x4.p0_0 = 0.415775
frequencies._aux.CF3x4.p0_1 = 0.250343
frequencies._aux.CF3x4.p0_2 = 0.652625
frequencies._aux.CF3x4.p1_0 = 0.399465
frequencies._aux.CF3x4.p1_1 = 0.28317
frequencies._aux.CF3x4.p1_2 = 0.391304
frequencies._aux.CF3x4.p2_0 = 0.253743
frequencies._aux.CF3x4.p2_1 = 0.314941
frequencies._aux.CF3x4.p2_2 = 0.521444
Optimization finished in 5 loop passes.
184 likelihood evaluation calls and 0 matrix exponentiations calls were made

Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
Model dIONygHy.model_MGREV assigned to Pig
Model dIONygHy.model_MGREV assigned to Cow
Model dIONygHy.model_MGREV assigned to Node3
Model dIONygHy.model_MGREV assigned to Horse
Model dIONygHy.model_MGREV assigned to Cat
Model dIONygHy.model_MGREV assigned to Node2
Model dIONygHy.model_MGREV assigned to RhMonkey
Model dIONygHy.model_MGREV assigned to Baboon
Model dIONygHy.model_MGREV assigned to Node9
Model dIONygHy.model_MGREV assigned to Human
Model dIONygHy.model_MGREV assigned to Chimp
Model dIONygHy.model_MGREV assigned to Node12
Model dIONygHy.model_MGREV assigned to Node8
Model dIONygHy.model_MGREV assigned to Node1
Model dIONygHy.model_MGREV assigned to Rat
Model dIONygHy.model_MGREV assigned to Mouse
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}

Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
Partition 0 reversible model flag computed as 1
Variable 'dIONygHy.dIONygHy.likelihoodFunction' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
Set GUI update interval to every 208-th LF evaluation.
Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

dIONygHy.model_MGREV.theta_CT = 1
dIONygHy.model_MGREV.theta_GT = 1
dIONygHy.model_MGREV.theta_CG = 1
dIONygHy.model_MGREV.theta_AC = 1
dIONygHy.model_MGREV.theta_AT = 1
dIONygHy.model_MGREV.omega_0 = 1
dIONygHy.tree_0.Pig.alpha = 0.000173063
dIONygHy.tree_0.Cow.alpha = 0.000186779
dIONygHy.tree_0.Node3.alpha = 1.15458e-05
dIONygHy.tree_0.Horse.alpha = 0.000174488
dIONygHy.tree_0.Cat.alpha = 0.000196799
dIONygHy.tree_0.Node2.alpha = 0.000173618
dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
dIONygHy.tree_0.Node9.alpha = 0.000140119
dIONygHy.tree_0.Human.alpha = 7.93383e-07
dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
dIONygHy.tree_0.Node12.alpha = 2.75759e-05
dIONygHy.tree_0.Node8.alpha = 4.67029e-05
dIONygHy.tree_0.Node1.alpha = 0.1
dIONygHy.tree_0.Rat.alpha = 8.26646e-05
dIONygHy.tree_0.Mouse.alpha = 0.000107933
Optimization finished in 35 loop passes.
3927 likelihood evaluation calls and 23083 matrix exponentiations calls were made

Row and/or column partition is empty. All the data will be used by default.
Set GUI update interval to every 2909-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

frequencies._aux.CF3x4.p0_0 = 0.415775
frequencies._aux.CF3x4.p0_1 = 0.250343
frequencies._aux.CF3x4.p0_2 = 0.652625
frequencies._aux.CF3x4.p1_0 = 0.399465
frequencies._aux.CF3x4.p1_1 = 0.28317
frequencies._aux.CF3x4.p1_2 = 0.391304
frequencies._aux.CF3x4.p2_0 = 0.253743
frequencies._aux.CF3x4.p2_1 = 0.314941
frequencies._aux.CF3x4.p2_2 = 0.521444
Optimization finished in 5 loop passes.
184 likelihood evaluation calls and 0 matrix exponentiations calls were made

Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
Model dIONygHy.model_MGREV assigned to Pig
Model dIONygHy.model_MGREV assigned to Cow
Model dIONygHy.model_MGREV assigned to Node3
Model dIONygHy.model_MGREV assigned to Horse
Model dIONygHy.model_MGREV assigned to Cat
Model dIONygHy.model_MGREV assigned to Node2
Model dIONygHy.model_MGREV assigned to RhMonkey
Model dIONygHy.model_MGREV assigned to Baboon
Model dIONygHy.model_MGREV assigned to Node9
Model dIONygHy.model_MGREV assigned to Human
Model dIONygHy.model_MGREV assigned to Chimp
Model dIONygHy.model_MGREV assigned to Node12
Model dIONygHy.model_MGREV assigned to Node8
Model dIONygHy.model_MGREV assigned to Node1
Model dIONygHy.model_MGREV assigned to Rat
Model dIONygHy.model_MGREV assigned to Mouse
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}

Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
Partition 0 reversible model flag computed as 1
Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
Set GUI update interval to every 269-th LF evaluation.
Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

dIONygHy.model_MGREV.theta_CG = 1
dIONygHy.model_MGREV.theta_AT = 1
dIONygHy.model_MGREV.theta_CT = 1
dIONygHy.model_MGREV.theta_GT = 1
dIONygHy.model_MGREV.theta_AC = 1
dIONygHy.model_MGREV.omega_0 = 1
dIONygHy.tree_0.Pig.alpha = 0.000173063
dIONygHy.tree_0.Cow.alpha = 0.000186779
dIONygHy.tree_0.Node3.alpha = 1.15458e-05
dIONygHy.tree_0.Horse.alpha = 0.000174488
dIONygHy.tree_0.Cat.alpha = 0.000196799
dIONygHy.tree_0.Node2.alpha = 0.000173618
dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
dIONygHy.tree_0.Node9.alpha = 0.000140119
dIONygHy.tree_0.Human.alpha = 7.93383e-07
dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
dIONygHy.tree_0.Node12.alpha = 2.75759e-05
dIONygHy.tree_0.Node8.alpha = 4.67029e-05
dIONygHy.tree_0.Node1.alpha = 0.1
dIONygHy.tree_0.Rat.alpha = 8.26646e-05
dIONygHy.tree_0.Mouse.alpha = 0.000107933
Optimization finished in 35 loop passes.
3276 likelihood evaluation calls and 21044 matrix exponentiations calls were made

Overwritten previously defined function:'IIsiGihg.rate_generator'
Overwritten previously defined function:'IIsiGihg.rate_generator'
Set GUI update interval to every 3023-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

frequencies._aux.CF3x4.p0_0 = 0.415775
frequencies._aux.CF3x4.p0_1 = 0.250343
frequencies._aux.CF3x4.p0_2 = 0.652625
frequencies._aux.CF3x4.p1_0 = 0.399465
frequencies._aux.CF3x4.p1_1 = 0.28317
frequencies._aux.CF3x4.p1_2 = 0.391304
frequencies._aux.CF3x4.p2_0 = 0.253743
frequencies._aux.CF3x4.p2_1 = 0.314941
frequencies._aux.CF3x4.p2_2 = 0.521444
Optimization finished in 5 loop passes.
184 likelihood evaluation calls and 0 matrix exponentiations calls were made

Variable 'busted.test_pi' was not initialized prior to being used
Overwritten previously defined function:'IIsiGihg.rate_generator'
Overwritten previously defined function:'IIsiGihg.rate_generator'
Overwritten previously defined function:'IIsiGihg.rate_generator'
Set GUI update interval to every 3010-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

frequencies._aux.CF3x4.p0_0 = 0.415775
frequencies._aux.CF3x4.p0_1 = 0.250343
frequencies._aux.CF3x4.p0_2 = 0.652625
frequencies._aux.CF3x4.p1_0 = 0.399465
frequencies._aux.CF3x4.p1_1 = 0.28317
frequencies._aux.CF3x4.p1_2 = 0.391304
frequencies._aux.CF3x4.p2_0 = 0.253743
frequencies._aux.CF3x4.p2_1 = 0.314941
frequencies._aux.CF3x4.p2_2 = 0.521444
Optimization finished in 5 loop passes.
184 likelihood evaluation calls and 0 matrix exponentiations calls were made

Variable 'busted.background_pi' was not initialized prior to being used
Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used
No nodel was assigned to Pig
No nodel was assigned to Cow
No nodel was assigned to Node3
No nodel was assigned to Horse
No nodel was assigned to Cat
No nodel was assigned to Node2
No nodel was assigned to RhMonkey
No nodel was assigned to Baboon
No nodel was assigned to Node9
No nodel was assigned to Human
No nodel was assigned to Chimp
No nodel was assigned to Node12
No nodel was assigned to Node8
No nodel was assigned to Node1
No nodel was assigned to Rat
No nodel was assigned to Mouse
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}

Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
Partition 0 is ASSUMED to have a reversible model
busted.test.theta_AG was already constrained in estimators.SetGlobals2
Variable 'CPXgZuSs.tree_id_0.Pig.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Pig.t=1.377886710534728
Variable 'CPXgZuSs.tree_id_0.Cow.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cow.t=1.774251775766245
Variable 'CPXgZuSs.tree_id_0.Node3.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node3.t=0.727900992785442
Variable 'CPXgZuSs.tree_id_0.Horse.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Horse.t=1.51058601207266
Variable 'CPXgZuSs.tree_id_0.Cat.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cat.t=1.957296993203762
Variable 'CPXgZuSs.tree_id_0.Node2.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node2.t=0.4612561973173576
Variable 'CPXgZuSs.tree_id_0.RhMonkey.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.RhMonkey.t=0.02659579655381833
Variable 'CPXgZuSs.tree_id_0.Baboon.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Baboon.t=0.01267390527294645
Variable 'CPXgZuSs.tree_id_0.Node9.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node9.t=0.1855677984720407
Variable 'CPXgZuSs.tree_id_0.Human.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Human.t=0
Variable 'CPXgZuSs.tree_id_0.Chimp.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Chimp.t=0.01307822802283968
Variable 'CPXgZuSs.tree_id_0.Node12.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node12.t=0.1279673910082466
Variable 'CPXgZuSs.tree_id_0.Node8.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node8.t=0.7824909790907859
Variable 'CPXgZuSs.tree_id_0.Node1.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node1.t=2.034207610785829
Variable 'CPXgZuSs.tree_id_0.Rat.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Rat.t=0.4799151894651191
Variable 'CPXgZuSs.tree_id_0.Mouse.t' was not initialized prior to being used
models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Mouse.t=0.859781481367942
Variable 'CPXgZuSs.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
Set GUI update interval to every 17-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

busted.test.theta_AC = 0.575889
busted.test.theta_AT = 0.266515
busted.test.omega1 = 0
busted.test.bsrel_mixture_aux_0 = 0.7
busted.test.theta_CG = 0.470944
busted.test.omega3 = 9.52381
busted.test.omega2 = 0.238095
busted.test.theta_CT = 0.973284
busted.test.bsrel_mixture_aux_1 = 0.666667
busted.test.theta_GT = 0.315964
CPXgZuSs.tree_id_0.Pig.t = 1.37789
CPXgZuSs.tree_id_0.Cow.t = 1.77425
CPXgZuSs.tree_id_0.Node3.t = 0.727901
CPXgZuSs.tree_id_0.Horse.t = 1.51059
CPXgZuSs.tree_id_0.Cat.t = 1.9573
CPXgZuSs.tree_id_0.Node2.t = 0.461256
CPXgZuSs.tree_id_0.RhMonkey.t = 0.0265958
CPXgZuSs.tree_id_0.Baboon.t = 0.0126739
CPXgZuSs.tree_id_0.Node9.t = 0.185568
CPXgZuSs.tree_id_0.Human.t = 0
CPXgZuSs.tree_id_0.Chimp.t = 0.0130782
CPXgZuSs.tree_id_0.Node12.t = 0.127967
CPXgZuSs.tree_id_0.Node8.t = 0.782491
CPXgZuSs.tree_id_0.Node1.t = 2.03421
CPXgZuSs.tree_id_0.Rat.t = 0.479915
CPXgZuSs.tree_id_0.Mouse.t = 0.859781
Optimization finished in 26 loop passes.
2990 likelihood evaluation calls and 70968 matrix exponentiations calls were made

Variable 'KIGDLXKi.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
Set GUI update interval to every 28-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

busted.test.theta_AC = 0.468589
busted.test.omega1 = 0.210733
busted.test.bsrel_mixture_aux_0 = 0.412135
busted.test.theta_AT = 0.215633
busted.test.omega2 = 0.105287
busted.test.bsrel_mixture_aux_1 = 0.404693
busted.test.theta_CT = 0.973171
busted.test.theta_GT = 0.273282
busted.test.theta_CG = 0.415669
CPXgZuSs.tree_id_0.Pig.t = 0.410826
CPXgZuSs.tree_id_0.Cow.t = 0.555921
CPXgZuSs.tree_id_0.Node3.t = 0.241332
CPXgZuSs.tree_id_0.Horse.t = 0.483056
CPXgZuSs.tree_id_0.Cat.t = 0.61829
CPXgZuSs.tree_id_0.Node2.t = 0.117184
CPXgZuSs.tree_id_0.RhMonkey.t = 0.00689772
CPXgZuSs.tree_id_0.Baboon.t = 0.0034792
CPXgZuSs.tree_id_0.Node9.t = 0.051855
CPXgZuSs.tree_id_0.Human.t = 0
CPXgZuSs.tree_id_0.Chimp.t = 0.00344635
CPXgZuSs.tree_id_0.Node12.t = 0.0343399
CPXgZuSs.tree_id_0.Node8.t = 0.253166
CPXgZuSs.tree_id_0.Node1.t = 0.86218
CPXgZuSs.tree_id_0.Rat.t = 0.138343
CPXgZuSs.tree_id_0.Mouse.t = 0.279774
Optimization finished in 14 loop passes.
1338 likelihood evaluation calls and 35802 matrix exponentiations calls were made

Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used
author	stephenshank
date	Thu, 17 Jan 2019 14:10:34 -0500
parents	7f0a4907e2e4
children