Loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
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Loaded 'convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
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Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
Loaded 'libv3/models/codon/MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
Loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
Loaded '../tasks/genetic_code.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
Loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
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Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
Loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
Loaded 'GrabBag' from /usr/local/lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
Overwritten previously defined function:'_sortStringsAux'
Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
Already loaded 'DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
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Already loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
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Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'libv3/tasks/estimators.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
Already loaded '../models/model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
Loaded '../models/DNA/GTR.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
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Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'libv3/tasks/alignments.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'libv3/tasks/trees.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
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Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'TreeTools' from /usr/local/lib/hyphy/TemplateBatchFiles/TreeTools.ibf
Loaded 'modules/io_functions.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
Already loaded 'libv3/convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'modules/selection_lib.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
Loaded 'libv3/models/codon/BS_REL.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
Already loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
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Already loaded 'MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
Loaded '../../convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Already loaded 'libv3/convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
Loaded 'libv3/tasks/mpi.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
Already loaded '../models/parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used
Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used
Loaded 'modules/shared-load-file.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used
Already loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
Variable 'JOYpYPkv.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 '_thZqV_F.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.
Loaded 'modules/grid_compute.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
Variable 'QPmholqs.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 'MiVdxtWn.model_pi' was not initialized prior to being used
Model MiVdxtWn.model assigned to Pig
Model MiVdxtWn.model assigned to Cow
Model MiVdxtWn.model assigned to Node3
Model MiVdxtWn.model assigned to Horse
Model MiVdxtWn.model assigned to Cat
Model MiVdxtWn.model assigned to Node2
Model MiVdxtWn.model assigned to RhMonkey
Model MiVdxtWn.model assigned to Baboon
Model MiVdxtWn.model assigned to Node9
Model MiVdxtWn.model assigned to Human
Model MiVdxtWn.model assigned to Chimp
Model MiVdxtWn.model assigned to Node12
Model MiVdxtWn.model assigned to Node8
Model MiVdxtWn.model assigned to Node1
Model MiVdxtWn.model assigned to Rat
Model MiVdxtWn.model assigned to Mouse
The tips of the tree:MiVdxtWn.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 is ASSUMED to have a reversible model
Variable 'USE_LAST_RESULTS' was not initialized prior to being used
Variable 'MiVdxtWn.tree_0.Pig.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Pig.t=0.3974535884114245
Variable 'MiVdxtWn.tree_0.Cow.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Cow.t=0.5732857515739808
Variable 'MiVdxtWn.tree_0.Node3.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Node3.t=0.2285810062933711
Variable 'MiVdxtWn.tree_0.Horse.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Horse.t=0.445313802634098
Variable 'MiVdxtWn.tree_0.Cat.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Cat.t=0.7112847618952328
Variable 'MiVdxtWn.tree_0.Node2.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Node2.t=0.1574326532610344
Variable 'MiVdxtWn.tree_0.RhMonkey.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.RhMonkey.t=0.00541241057687097
Variable 'MiVdxtWn.tree_0.Baboon.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Baboon.t=0.008348273981595522
Variable 'MiVdxtWn.tree_0.Node9.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Node9.t=0.06106219833449517
Variable 'MiVdxtWn.tree_0.Human.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Human.t=0.01168167424258652
Variable 'MiVdxtWn.tree_0.Chimp.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Chimp.t=0.00214616181187092
Variable 'MiVdxtWn.tree_0.Node12.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Node12.t=0.03189158847602433
Variable 'MiVdxtWn.tree_0.Node8.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Node8.t=0.2735913110261884
Variable 'MiVdxtWn.tree_0.Node1.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Node1.t=0.9154145654683773
Variable 'MiVdxtWn.tree_0.Rat.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Rat.t=0.1368762373082833
Variable 'MiVdxtWn.tree_0.Mouse.t' was not initialized prior to being used
models.generic.SetBranchLength: MiVdxtWn.tree_0.Mouse.t=0.2630995612925615
Variable 'MiVdxtWn.MiVdxtWn.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 331-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

MiVdxtWn.model.theta_GT = 0.25
MiVdxtWn.model.theta_CG = 0.25
MiVdxtWn.model.theta_CT = 1
MiVdxtWn.model.theta_AT = 0.25
MiVdxtWn.model.theta_AC = 0.25
MiVdxtWn.tree_0.Pig.t = 0.397454
MiVdxtWn.tree_0.Cow.t = 0.573286
MiVdxtWn.tree_0.Node3.t = 0.228581
MiVdxtWn.tree_0.Horse.t = 0.445314
MiVdxtWn.tree_0.Cat.t = 0.711285
MiVdxtWn.tree_0.Node2.t = 0.157433
MiVdxtWn.tree_0.RhMonkey.t = 0.00541241
MiVdxtWn.tree_0.Baboon.t = 0.00834827
MiVdxtWn.tree_0.Node9.t = 0.0610622
MiVdxtWn.tree_0.Human.t = 0.0116817
MiVdxtWn.tree_0.Chimp.t = 0.00214616
MiVdxtWn.tree_0.Node12.t = 0.0318916
MiVdxtWn.tree_0.Node8.t = 0.273591
MiVdxtWn.tree_0.Node1.t = 0.915415
MiVdxtWn.tree_0.Rat.t = 0.136876
MiVdxtWn.tree_0.Mouse.t = 0.2631
Optimization finished in 24 loop passes.
1467 likelihood evaluation calls and 10507 matrix exponentiations calls were made

Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used
Variable 'MiVdxtWn.option' was not initialized prior to being used
Variable 'relax.terms.json.nucleotide_gtr' was not initialized prior to being used
Variable 'Unknown' was not initialized prior to being used
Variable 'SRnFPBcA.initial_value' was not initialized prior to being used
Variable 'FYuAtbni.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 2879-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 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used
Model FYuAtbni.model_MGREV assigned to Pig
Model FYuAtbni.model_MGREV assigned to Cow
Model FYuAtbni.model_MGREV assigned to Node3
Model FYuAtbni.model_MGREV assigned to Horse
Model FYuAtbni.model_MGREV assigned to Cat
Model FYuAtbni.model_MGREV assigned to Node2
Model FYuAtbni.model_MGREV assigned to RhMonkey
Model FYuAtbni.model_MGREV assigned to Baboon
Model FYuAtbni.model_MGREV assigned to Node9
Model FYuAtbni.model_MGREV assigned to Human
Model FYuAtbni.model_MGREV assigned to Chimp
Model FYuAtbni.model_MGREV assigned to Node12
Model FYuAtbni.model_MGREV assigned to Node8
Model FYuAtbni.model_MGREV assigned to Node1
Model FYuAtbni.model_MGREV assigned to Rat
Model FYuAtbni.model_MGREV assigned to Mouse
The tips of the tree:FYuAtbni.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 is ASSUMED to have a reversible model
Variable 'FYuAtbni.FYuAtbni.likelihoodFunction' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used
Variable 'FYuAtbni.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 187-th LF evaluation.
Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618
Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05
Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063
Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779
Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488
Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799
Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05
Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119
Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06
Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06
Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05
Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07
Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06
Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05
Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

FYuAtbni.model_MGREV.theta_GT = 1
FYuAtbni.model_MGREV.theta_CT = 1
FYuAtbni.model_MGREV.theta_AC = 1
FYuAtbni.model_MGREV.theta_CG = 1
FYuAtbni.model_MGREV.theta_AT = 1
FYuAtbni.model_MGREV.omega_0 = 1
FYuAtbni.model_MGREV.omega_1 = 1
FYuAtbni.tree_0.Pig.alpha = 0.000173063
FYuAtbni.tree_0.Cow.alpha = 0.000186779
FYuAtbni.tree_0.Node3.alpha = 1.15458e-05
FYuAtbni.tree_0.Horse.alpha = 0.000174488
FYuAtbni.tree_0.Cat.alpha = 0.000196799
FYuAtbni.tree_0.Node2.alpha = 0.000173618
FYuAtbni.model_MGREV.omega_2 = 1
FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06
FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06
FYuAtbni.tree_0.Node9.alpha = 0.000140119
FYuAtbni.tree_0.Human.alpha = 7.93383e-07
FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06
FYuAtbni.tree_0.Node12.alpha = 2.75759e-05
FYuAtbni.tree_0.Node8.alpha = 4.67029e-05
FYuAtbni.tree_0.Node1.alpha = 0.1
FYuAtbni.tree_0.Rat.alpha = 8.26646e-05
FYuAtbni.tree_0.Mouse.alpha = 0.000107933
Optimization finished in 37 loop passes.
3110 likelihood evaluation calls and 18285 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 2926-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 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used
Model FYuAtbni.model_MGREV assigned to Pig
Model FYuAtbni.model_MGREV assigned to Cow
Model FYuAtbni.model_MGREV assigned to Node3
Model FYuAtbni.model_MGREV assigned to Horse
Model FYuAtbni.model_MGREV assigned to Cat
Model FYuAtbni.model_MGREV assigned to Node2
Model FYuAtbni.model_MGREV assigned to RhMonkey
Model FYuAtbni.model_MGREV assigned to Baboon
Model FYuAtbni.model_MGREV assigned to Node9
Model FYuAtbni.model_MGREV assigned to Human
Model FYuAtbni.model_MGREV assigned to Chimp
Model FYuAtbni.model_MGREV assigned to Node12
Model FYuAtbni.model_MGREV assigned to Node8
Model FYuAtbni.model_MGREV assigned to Node1
Model FYuAtbni.model_MGREV assigned to Rat
Model FYuAtbni.model_MGREV assigned to Mouse
The tips of the tree:FYuAtbni.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 is ASSUMED to have a reversible model
Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used
Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used
Variable 'FYuAtbni.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 285-th LF evaluation.
Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618
Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05
Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063
Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779
Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488
Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799
Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05
Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119
Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06
Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06
Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05
Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07
Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06
Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05
Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

FYuAtbni.model_MGREV.theta_CG = 1
FYuAtbni.model_MGREV.theta_AT = 1
FYuAtbni.model_MGREV.theta_CT = 1
FYuAtbni.model_MGREV.theta_GT = 1
FYuAtbni.model_MGREV.theta_AC = 1
FYuAtbni.model_MGREV.omega_0 = 1
FYuAtbni.model_MGREV.omega_1 = 1
FYuAtbni.tree_0.Pig.alpha = 0.000173063
FYuAtbni.tree_0.Cow.alpha = 0.000186779
FYuAtbni.tree_0.Node3.alpha = 1.15458e-05
FYuAtbni.tree_0.Horse.alpha = 0.000174488
FYuAtbni.tree_0.Cat.alpha = 0.000196799
FYuAtbni.tree_0.Node2.alpha = 0.000173618
FYuAtbni.model_MGREV.omega_2 = 1
FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06
FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06
FYuAtbni.tree_0.Node9.alpha = 0.000140119
FYuAtbni.tree_0.Human.alpha = 7.93383e-07
FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06
FYuAtbni.tree_0.Node12.alpha = 2.75759e-05
FYuAtbni.tree_0.Node8.alpha = 4.67029e-05
FYuAtbni.tree_0.Node1.alpha = 0.1
FYuAtbni.tree_0.Rat.alpha = 8.26646e-05
FYuAtbni.tree_0.Mouse.alpha = 0.000107933
Optimization finished in 30 loop passes.
3225 likelihood evaluation calls and 18018 matrix exponentiations calls were made

Overwritten previously defined function:'GpmgdDcy.rate_generator'
Overwritten previously defined function:'GpmgdDcy.rate_generator'
Set GUI update interval to every 2992-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 'relax.test_pi' was not initialized prior to being used
Overwritten previously defined function:'GpmgdDcy.rate_generator'
Overwritten previously defined function:'GpmgdDcy.rate_generator'
Overwritten previously defined function:'GpmgdDcy.rate_generator'
Set GUI update interval to every 2912-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 'relax.reference_pi' was not initialized prior to being used
Overwritten previously defined function:'GpmgdDcy.rate_generator'
Overwritten previously defined function:'GpmgdDcy.rate_generator'
Overwritten previously defined function:'GpmgdDcy.rate_generator'
Set GUI update interval to every 2827-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 'relax.unclassified_pi' 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:RPGDJipv.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
relax.reference.theta_AC was already constrained in estimators.SetGlobals2
relax.reference.theta_AG was already constrained in estimators.SetGlobals2
relax.reference.theta_AT was already constrained in estimators.SetGlobals2
relax.reference.theta_CG was already constrained in estimators.SetGlobals2
relax.reference.theta_CT was already constrained in estimators.SetGlobals2
relax.reference.theta_GT was already constrained in estimators.SetGlobals2
relax.test.theta_AG was already constrained in estimators.SetGlobals2
relax.unclassified.theta_AC was already constrained in estimators.SetGlobals2
relax.unclassified.theta_AG was already constrained in estimators.SetGlobals2
relax.unclassified.theta_AT was already constrained in estimators.SetGlobals2
relax.unclassified.theta_CG was already constrained in estimators.SetGlobals2
relax.unclassified.theta_CT was already constrained in estimators.SetGlobals2
relax.unclassified.theta_GT was already constrained in estimators.SetGlobals2
Variable 'RPGDJipv.tree_id_0.Pig.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Pig.t=1.375151388677762
Variable 'RPGDJipv.tree_id_0.Cow.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cow.t=1.781953803671641
Variable 'RPGDJipv.tree_id_0.Node3.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node3.t=0.7179600319187995
Variable 'RPGDJipv.tree_id_0.Horse.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Horse.t=1.501071819834825
Variable 'RPGDJipv.tree_id_0.Cat.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cat.t=1.973271183104609
Variable 'RPGDJipv.tree_id_0.Node2.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node2.t=0.4461859649428869
Variable 'RPGDJipv.tree_id_0.RhMonkey.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.RhMonkey.t=0.02655846610185887
Variable 'RPGDJipv.tree_id_0.Baboon.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Baboon.t=0.01259838399210765
Variable 'RPGDJipv.tree_id_0.Node9.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node9.t=0.1891887653227436
Variable 'RPGDJipv.tree_id_0.Human.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Human.t=0
Variable 'RPGDJipv.tree_id_0.Chimp.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Chimp.t=0.01302152547854442
Variable 'RPGDJipv.tree_id_0.Node12.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node12.t=0.1235892304460588
Variable 'RPGDJipv.tree_id_0.Node8.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node8.t=0.8108545924902142
Variable 'RPGDJipv.tree_id_0.Node1.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node1.t=2.056868575380766
Variable 'RPGDJipv.tree_id_0.Rat.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Rat.t=0.485173250741015
Variable 'RPGDJipv.tree_id_0.Mouse.t' was not initialized prior to being used
models.generic.SetBranchLength: RPGDJipv.tree_id_0.Mouse.t=0.8522851263393678
Variable 'RPGDJipv.RPGDJipv.likelihoodFunction' was not initialized prior to being used
Set GUI update interval to every 26-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

relax.test.theta_GT = 0.315401
relax.test.theta_CT = 0.98654
relax.test.theta_AC = 0.578523
relax.test.theta_CG = 0.469908
relax.test.theta_AT = 0.267066
relax.reference.bsrel_mixture_aux_1 = 0.818182
relax.reference.omega1 = 0.145496
relax.reference.omega2 = 0.4601
relax.reference.bsrel_mixture_aux_0 = 0.45
relax.reference.omega3 = 7.27482
relax.unclassified.omega3 = 1
relax.unclassified.bsrel_mixture_aux_1 = 0.5
relax.unclassified.omega2 = 1
relax.unclassified.omega1 = 1
relax.K = 1
relax.unclassified.bsrel_mixture_aux_0 = 0.5
RPGDJipv.tree_id_0.Pig.t = 1.37515
RPGDJipv.tree_id_0.Cow.t = 1.78195
RPGDJipv.tree_id_0.Node3.t = 0.71796
RPGDJipv.tree_id_0.Horse.t = 1.50107
RPGDJipv.tree_id_0.Cat.t = 1.97327
RPGDJipv.tree_id_0.Node2.t = 0.446186
RPGDJipv.tree_id_0.RhMonkey.t = 0.0265585
RPGDJipv.tree_id_0.Baboon.t = 0.0125984
RPGDJipv.tree_id_0.Node9.t = 0.189189
RPGDJipv.tree_id_0.Human.t = 0
RPGDJipv.tree_id_0.Chimp.t = 0.0130215
RPGDJipv.tree_id_0.Node12.t = 0.123589
RPGDJipv.tree_id_0.Node8.t = 0.810855
RPGDJipv.tree_id_0.Node1.t = 2.05687
RPGDJipv.tree_id_0.Rat.t = 0.485173
RPGDJipv.tree_id_0.Mouse.t = 0.852285
Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
Optimization finished in 156 loop passes.
19208 likelihood evaluation calls and 408312 matrix exponentiations calls were made

Variable 'MPI_NODE_COUNT' was not initialized prior to being used
Variable 'esPQwqFL.RPGDJipv.likelihoodFunction' was not initialized prior to being used
Set GUI update interval to every 24-th LF evaluation.
Optimization settings:
	OPTIMIZATION_METHOD = 4
	OPTIMIZATION_PRECISION = 0.001
	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000

Initial parameter values

relax.test.theta_GT = 0.272534
relax.test.theta_CT = 0.989376
relax.test.theta_AC = 0.472659
relax.test.theta_CG = 0.409729
relax.test.theta_AT = 0.213063
relax.reference.omega2 = 0
relax.reference.omega3 = 1.81261
relax.reference.bsrel_mixture_aux_1 = 0.398417
relax.reference.bsrel_mixture_aux_0 = 0.26934
relax.reference.omega1 = 0
relax.unclassified.omega2 = 3.8108
relax.unclassified.bsrel_mixture_aux_1 = 0.965815
relax.unclassified.omega3 = 88.0589
relax.unclassified.omega1 = 0
relax.unclassified.bsrel_mixture_aux_0 = 0.488814
RPGDJipv.tree_id_0.Pig.t = 0.288673
RPGDJipv.tree_id_0.Cow.t = 0.415456
RPGDJipv.tree_id_0.Node3.t = 0.165342
RPGDJipv.tree_id_0.Horse.t = 0.373597
RPGDJipv.tree_id_0.Cat.t = 0.4862
RPGDJipv.tree_id_0.Node2.t = 0.071002
RPGDJipv.tree_id_0.RhMonkey.t = 0.0109335
RPGDJipv.tree_id_0.Baboon.t = 0.00559127
RPGDJipv.tree_id_0.Node9.t = 0.0891892
RPGDJipv.tree_id_0.Human.t = 0
RPGDJipv.tree_id_0.Chimp.t = 0.0054891
RPGDJipv.tree_id_0.Node12.t = 0.0161348
RPGDJipv.tree_id_0.Node8.t = 0.405701
RPGDJipv.tree_id_0.Node1.t = 1.12055
RPGDJipv.tree_id_0.Rat.t = 0.217643
RPGDJipv.tree_id_0.Mouse.t = 0.392946
Optimization finished in 62 loop passes.
6270 likelihood evaluation calls and 146691 matrix exponentiations calls were made

Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used