Status
±
Terminal Output
| Builder file created | |
| Configuration file | |
| ProBound run | |
| Sequence logos |
Terminal output
Pipeline Output:
> Converts the configuration file to work on run server, checks input OK > Builds configuration file OK > Runs ProBound OK > Runs Model Viewer OK
Configuration Builder File
±
ProBound builder configuration file:
[{"function": "optimizerSetting", "pseudocount": 50, "nThreads": 10, "lambdaL2": 1e-06}, {"function": "lbfgsSettings", "maxIters": 2000}, {"function": "addTable", "leftFlank": "TAGTSVAGQSGQ", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/7051bfc72e49/countTable.0.tsv.gz", "rightFlank": "GGQSGQSGDYNK", "inputFileType": "tsv.gz", "variableRegionLength": 11}, {"function": "addTable", "leftFlank": "TAGTSVAGQSGQ", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/7051bfc72e49/countTable.1.tsv.gz", "rightFlank": "GGQSGQSGDYNK", "inputFileType": "tsv.gz", "variableRegionLength": 11}, {"function": "addTable", "leftFlank": "TAGTSVAGQSGQ", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/7051bfc72e49/countTable.2.tsv.gz", "rightFlank": "GGQSGQSGDYNK", "inputFileType": "tsv.gz", "variableRegionLength": 11}, {"function": "addSELEX", "concentration": 0.25, "modelType": "ExponentialKinetics"}, {"function": "addSELEX", "concentration": 1, "modelType": "ExponentialKinetics"}, {"function": "addSELEX", "concentration": 3, "modelType": "ExponentialKinetics"}, {"function": "setAlphabet", "letterComplement": "A-A,C-C,D-D,E-E,F-F,G-G,H-H,I-I,K-K,L-L,M-M,N-N,P-P,Q-Q,R-R,S-S,T-T,V-V,W-W,Y-Y", "letterOrder": "ACDEFGHIKLMNPQRSTVWY"}, {"function": "addNS"}, {"function": "addBindingMode", "flankLength": 3, "singleStrand": true, "dinucleotideDistance": 7, "size": 7}, {"function": "bindingModeConstraints", "index": 1, "experimentSpecificActivity": false}, {"function": "symmetry", "index": 1, "symmetryString": "abc.efg"}, {"function": "bindingModeSeed", "index": 1, "seedScale": 10, "mononucleotideString": "...Y..."}, {"function": "enrichmentModelConstraints", "index": -1, "fitDelta": [false, false]}, {"function": "enrichmentModelSeed", "index": -1, "delta": [0, -15]}, {"function": "output", "outputPath": "jobs/7051bfc72e49", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]Configuration File
±
ProBound configuration file:
{
"modelSeeding": {
"enrichmentModel": [
{
"delta": [
0,
-15
],
"index": -1
},
{
"delta": [
0,
-15
],
"index": -1
},
{
"delta": [
0,
-15
],
"index": -1
}
],
"bindingModes": [
{"seedScale": 1},
{
"seedScale": 10,
"mononucleotideString": "...Y..."
}
]
},
"optimizerSetting": {
"nThreads": 10,
"likelihoodThreshold": 0,
"lambdaL2": 1.0E-6,
"pseudocount": 50,
"patternSearchSettings": {},
"minimizerType": "lbfgs",
"nRetries": 3,
"hkSettings": {},
"output": {
"storeHessian": false,
"outputPath": "jobs/7051bfc72e49",
"printTrajectory": false,
"baseName": "fit",
"printPSAM": false,
"verbose": true
},
"lbfgsSettings": {
"memory": 100,
"convergence": 1.0E-7,
"MCSearch": true,
"maxIters": 2000
},
"sgdSettings": {},
"fixedLibrarySize": false,
"expBound": 40,
"slbfgs_plsSettings": {},
"slbfgsSettings": {}
},
"modelSettings": {
"enrichmentModel": [
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 0.25,
"modelType": "ExponentialKinetics",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "ExponentialKinetics",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 3,
"modelType": "ExponentialKinetics",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
}
],
"letterOrder": "ACDEFGHIKLMNPQRSTVWY",
"countTable": [
{
"leftFlank": "TAGTSVAGQSGQ",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 11,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "GGQSGQSGDYNK",
"countTableFile": "jobs/7051bfc72e49/countTable.0.tsv.gz"
},
{
"leftFlank": "TAGTSVAGQSGQ",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 11,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "GGQSGQSGDYNK",
"countTableFile": "jobs/7051bfc72e49/countTable.1.tsv.gz"
},
{
"leftFlank": "TAGTSVAGQSGQ",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 11,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "GGQSGQSGDYNK",
"countTableFile": "jobs/7051bfc72e49/countTable.2.tsv.gz"
}
],
"bindingModeInteractions": [],
"bindingModes": [
{
"size": 0,
"fitLogActivity": true,
"flankLength": 0,
"dinucleotideDistance": 0,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 7,
"fitLogActivity": true,
"flankLength": 3,
"dinucleotideDistance": 7,
"positionBias": false,
"singleStrand": true,
"modifications": []
}
],
"letterComplement": "A-A,C-C,D-D,E-E,F-F,G-G,H-H,I-I,K-K,L-L,M-M,N-N,P-P,Q-Q,R-R,S-S,T-T,V-V,W-W,Y-Y"
},
"modelFittingConstraints": {
"enrichmentModel": [
{
"fitDelta": [
false,
false
],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [
false,
false
],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [
false,
false
],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
}
],
"nShifts": 0,
"countTable": [
{},
{},
{}
],
"addBindingModesSequentially": true,
"flankLengths": [0],
"bindingModeInteractions": [],
"singleModeLengthSweep": false,
"bindingModes": [
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
},
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"symmetryString": "abc.efg",
"optimizeFlankLength": false,
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": false,
"optimizeSize": false
}
]
}
}Probound Text Output
±
Output from ProBound:
> Reading configuration JSON object and validating general schema.
> Validating configuration schema.
{"enrichmentModel":[{"fitDelta":[false,false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false,false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false,false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}],"nShifts":0,"countTable":[{},{},{}],"addBindingModesSequentially":true,"flankLengths":[0],"bindingModeInteractions":[],"singleModeLengthSweep":false,"bindingModes":[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"abc.efg","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":false,"optimizeSize":false}]}
Entry=bindingModes, aEntry=[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"abc.efg","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":false,"optimizeSize":false}]
Entry=bindingModeInteractions, aEntry=[]
Entry=countTable, aEntry=[{},{},{}]
Entry=enrichmentModel, aEntry=[{"fitDelta":[false,false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false,false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false,false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}]
> Builds likelihood object.
>> Creating CombinedLikelihood object.
Alphabet
========
Letter Complement: A-A,C-C,D-D,E-E,F-F,G-G,H-H,I-I,K-K,L-L,M-M,N-N,P-P,Q-Q,R-R,S-S,T-T,V-V,W-W,Y-Y
Letter Order: ACDEFGHIKLMNPQRSTVWY
Optimizer settings:
===================
lambdaL2 = 1.0E-6
pseudocount = 50.0
expBound = 40.0
fixedLibrarySize = false
>> Determining fitting order.
Summary of experiments
======================
Experiment 0:
-------------
Count table: Count table 0
Enrichment model: Exponential Kinetics enrichment model 0
Concentration: 0.25
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 1:
-------------
Count table: Count table 1
Enrichment model: Exponential Kinetics enrichment model 1
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 2:
-------------
Count table: Count table 2
Enrichment model: Exponential Kinetics enrichment model 2
Concentration: 3.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
> Builds optimizer.
> Using LBFGS.
> Starting optimization.
==================================
== Starts fiting Binding mode 0 ==
==================================
> Optimizing h (component0-0-h).
>> Starting new optimization: component0-0-h. (2021-05-21 16:16:07.328).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 13.795251627949309
gradient = {0.8727,-0.8727,0.6910,-0.6910,0.6628,-0.6628}
gradient norm = 1.8321251336960593
Starting Function Value: 13.795251627949309
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 4.982583060798526 5.000000000000000 2.729071234295657 1.539160917893324
2 5 3.312869059382126 7.615856085441662 0.248461037593013 0.629822216279532
3 6 1.944173118041165 2.483059724165376 1.000000000000000 0.409803644236072
4 8 1.665068139557254 1.024243205550869 0.222491106688380 0.123169704494274
5 9 1.638614152559001 0.477839930786558 1.000000000000000 0.054268275946298
6 10 1.634582399110403 0.138339421735772 1.000000000000000 0.007953941593811
7 11 1.634493387113997 0.025445426009120 1.000000000000000 0.000844767646038
8 12 1.634492436718542 0.002820799245418 1.000000000000000 0.000177555310882
9 13 1.634492399398960 0.000426277031382 1.000000000000000 0.000005183138537
10 14 1.634492399352815 0.000426277031382 1.000000000000000 0.000000717455144
Convergence criteria met.
After: gradient norm = 7.174551440260777E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-4.0592,4.0592}
Count Table 1:
---------------
h: {-3.4945,3.4945}
Count Table 2:
---------------
h: {-3.4299,3.4299}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-4.7875,-4.7875}
Activity(exp=1): {-6.1738,-6.1738}
Activity(exp=2): {-7.2724,-7.2724}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): 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Dinucleotide(d=4): 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Dinucleotide(d=5): 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Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
> Initial optimization (component0-1-f0).
>> Starting new optimization: component0-1-f0. (2021-05-21 16:16:10.189).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5]]},{}]}
Value and gradient before optimization:
=======================================
value = 1.634492399352832
gradient = {-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 4.039600196626832E-5
Starting Function Value: 1.634492399352832
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 1.634492393635870 0.000282233282460 6.986663746974583 0.000072288103789
2 4 1.634492385142226 0.000247962810494 1.000000000000000 0.000069835369627
3 5 1.634492159766741 0.008767889672204 1.000000000000000 0.000240877060612
4 6 1.634491775606391 0.017725159886267 1.000000000000000 0.000478342043988
5 7 1.634490558546614 0.061427321453521 1.000000000000000 0.000953699196628
6 8 1.634487612058341 0.156679431087623 1.000000000000000 0.001666155536698
7 9 1.634479846847577 0.427937246188562 1.000000000000000 0.002802770466641
8 10 1.634460946649382 1.074065881035225 1.000000000000000 0.004498961331146
9 11 1.634420340960515 2.483924052962391 1.000000000000000 0.006825778876317
10 13 1.634397370166967 1.186354035850995 0.322151321288150 0.007466840837173
11 15 1.634360741984603 1.651614650573410 0.343107936993843 0.007955759950034
12 16 1.634319623539269 2.148575842507885 1.000000000000000 0.009138985021882
13 18 1.634278211434948 0.577586229659979 0.405533569448681 0.003998010591083
14 19 1.634262575774458 0.405879808225193 1.000000000000000 0.002203243737760
15 20 1.634255329967165 0.304731286360715 1.000000000000000 0.001331392531128
16 21 1.634249574455080 0.913227713618705 1.000000000000000 0.003396159295201
17 22 1.634243333629640 0.166976141434899 1.000000000000000 0.001299107633707
18 23 1.634237636967312 0.360245931669514 1.000000000000000 0.001052671981995
19 25 1.634232663838257 0.458376890055584 0.248268107193059 0.001616251800134
20 26 1.634229126340708 0.616529388214919 1.000000000000000 0.002761732074154
21 27 1.634225059759492 0.054783543039905 1.000000000000000 0.001354159799486
22 28 1.634220931658437 0.259430791454523 1.000000000000000 0.000710648916282
23 30 1.634219166724983 0.231457295319068 0.304362913079279 0.001231445886642
24 31 1.634217158516782 0.237658950035794 1.000000000000000 0.001463013611880
25 32 1.634214960721590 0.119132891518723 1.000000000000000 0.000974655040762
26 34 1.634212757807475 0.299640541235428 0.534149563771263 0.001330581894144
27 35 1.634209937909112 0.262100673195098 1.000000000000000 0.001153761759790
28 36 1.634209073402177 0.072075270319776 1.000000000000000 0.001057890933708
29 37 1.634206843046630 0.378659203911438 1.000000000000000 0.001508014841005
30 38 1.634206156024413 0.149626820079800 1.000000000000000 0.000201049463238
31 39 1.634205043850030 0.141106658876043 1.000000000000000 0.000330463575388
32 41 1.634204305468313 0.141646360221287 0.221808191946290 0.000745914198941
33 42 1.634203625140837 0.149123773508309 1.000000000000000 0.001033284806989
34 43 1.634202345279563 0.104647111037243 1.000000000000000 0.000701353484540
35 44 1.634200878075007 0.209187284963927 1.000000000000000 0.000716513851743
36 45 1.634199387356175 0.176279604650115 1.000000000000000 0.000425664062731
37 47 1.634198356026004 0.158915158222000 0.187050278470997 0.000409021679587
38 49 1.634198127182061 0.073386733569472 0.291429534596022 0.000638511456163
39 50 1.634197683928189 0.070335311483469 1.000000000000000 0.000610761977228
40 51 1.634196963309930 0.101003544934648 1.000000000000000 0.000468851191734
41 52 1.634196561003104 0.171797257098111 1.000000000000000 0.000879109302045
42 53 1.634195450889920 0.081398238022179 1.000000000000000 0.000267065898356
43 55 1.634194999126383 0.120613570221605 0.451959864912626 0.000476773635208
44 56 1.634194539226975 0.137406572200687 1.000000000000000 0.000659679125496
45 57 1.634193993729649 0.052332120452645 1.000000000000000 0.000335261870741
46 58 1.634193578671056 0.151436788392820 1.000000000000000 0.000611408306020
47 59 1.634193236282236 0.021009737708660 1.000000000000000 0.000323391093364
48 61 1.634192985797129 0.074671726065001 0.408605268810234 0.000389112361968
49 62 1.634192516048246 0.107791706199747 1.000000000000000 0.000302661381755
50 63 1.634192288203250 0.127373267379150 1.000000000000000 0.000558819461933
51 64 1.634191600155324 0.113536069577942 1.000000000000000 0.000141721798018
52 66 1.634191504299585 0.055874835846895 0.352881123442243 0.000315830188068
53 67 1.634191226282071 0.117557201837711 1.000000000000000 0.000412885703331
54 68 1.634190906243102 0.056661230299392 1.000000000000000 0.000095135678895
55 70 1.634190722379854 0.084703820379375 0.422798217602261 0.000218551996312
56 72 1.634190642485148 0.060729068323847 0.508477619849586 0.000337713975069
57 73 1.634190471431174 0.047263340296268 1.000000000000000 0.000232042141711
58 74 1.634190279535724 0.073819589587532 1.000000000000000 0.000162602080178
59 75 1.634190125681196 0.106198810444640 1.000000000000000 0.000287029752036
60 76 1.634189786141644 0.150876699356060 1.000000000000000 0.000107483424422
61 78 1.634189759678649 0.026011743132019 0.109030058360610 0.000158312709350
62 79 1.634189696173407 0.052012423739337 1.000000000000000 0.000189447576703
63 80 1.634189611764891 0.060951015538225 1.000000000000000 0.000177030848494
64 81 1.634189550840685 0.031751520692332 1.000000000000000 0.000106415515415
65 83 1.634189499412156 0.059076073294791 0.414696704919785 0.000154143808882
66 84 1.634189470226657 0.075680387294965 1.000000000000000 0.000250267329072
67 85 1.634189407863379 0.004611671729638 1.000000000000000 0.000063617735979
68 86 1.634189379361883 0.036569891052360 1.000000000000000 0.000083996495339
69 88 1.634189349917090 0.053851749588377 0.475647394572751 0.000133030752479
70 89 1.634189316788006 0.041179606370473 1.000000000000000 0.000107495061192
71 90 1.634189286873513 0.032965391366602 1.000000000000000 0.000027455090155
72 92 1.634189270276354 0.038466548770057 0.284211526794247 0.000054389186970
73 94 1.634189262722054 0.026581128796652 0.455303386057515 0.000077375309985
74 95 1.634189250288805 0.031431822666783 1.000000000000000 0.000065816340426
75 96 1.634189238875387 0.025013492265815 1.000000000000000 0.000025865189872
76 98 1.634189233740518 0.031982921376358 0.517230240126681 0.000049606774705
77 99 1.634189228020197 0.023962155341406 1.000000000000000 0.000030333685812
78 100 1.634189225173617 0.016510678466437 1.000000000000000 0.000006548736553
79 102 1.634189224192866 0.017406513139006 0.410845950858333 0.000019082349724
80 103 1.634189223355241 0.012932426924871 1.000000000000000 0.000009855391053
81 104 1.634189223114736 0.006148974255667 1.000000000000000 0.000000861327518
82 105 1.634189223079043 0.007370722821042 1.000000000000000 0.000002941680058
83 106 1.634189223059923 0.001193104102757 1.000000000000000 0.000000716322906
84 107 1.634189223056072 0.000060219076633 1.000000000000000 0.000001234867554
85 108 1.634189223042858 0.000182805535987 1.000000000000000 0.000002790917063
86 109 1.634189223012611 0.000310713608118 1.000000000000000 0.000005097560233
87 110 1.634189222929482 0.000664523365051 1.000000000000000 0.000009059192289
88 111 1.634189222715981 0.001444501951994 1.000000000000000 0.000015294748013
89 112 1.634189222151789 0.003607049835121 1.000000000000000 0.000025199595688
90 113 1.634189220616763 0.010491602600050 1.000000000000000 0.000039610434023
91 114 1.634189215808364 0.044107211184406 1.000000000000000 0.000049677994686
92 115 1.634189211392130 0.046040431570690 1.000000000000000 0.000081805560963
93 116 1.634189195773232 0.060120269301485 1.000000000000000 0.000147033231598
94 117 1.634189179007372 0.022233533986629 1.000000000000000 0.000103197694395
95 118 1.634189161709080 0.041531330293656 1.000000000000000 0.000050549542258
96 119 1.634189160025361 0.004234481397285 1.000000000000000 0.000031697628729
97 120 1.634189156966442 0.016288265604186 1.000000000000000 0.000029194366042
98 122 1.634189151755692 0.024467918030389 0.328428961079022 0.000046850239504
99 123 1.634189147976138 0.036245825835938 1.000000000000000 0.000058066008969
100 124 1.634189142856622 0.002971449680791 1.000000000000000 0.000015876336460
101 125 1.634189139754093 0.017587466786542 1.000000000000000 0.000016747287773
102 126 1.634189136882674 0.029684255390816 1.000000000000000 0.000026042365230
103 127 1.634189135110191 0.012082676353368 1.000000000000000 0.000004141063142
104 128 1.634189134650026 0.018987791445910 1.000000000000000 0.000011793755244
105 129 1.634189134449951 0.002204135106745 1.000000000000000 0.000001000855319
106 130 1.634189134409044 0.004192813179948 1.000000000000000 0.000000679818242
107 131 1.634189134404311 0.001760585611027 1.000000000000000 0.000000613498272
108 132 1.634189134403195 0.000302472528682 1.000000000000000 0.000000774881562
109 133 1.634189134398284 0.001253621029239 1.000000000000000 0.000001170319242
110 134 1.634189134393286 0.001273754571194 1.000000000000000 0.000001166240952
111 135 1.634189134386709 0.001373375697291 1.000000000000000 0.000000473493297
112 136 1.634189134383904 0.000920134961274 1.000000000000000 0.000000395827765
113 137 1.634189134383117 0.000339862881535 1.000000000000000 0.000000666515476
114 138 1.634189134381977 0.000418528952063 1.000000000000000 0.000000977474983
115 139 1.634189134379543 0.000570466088120 1.000000000000000 0.000001397364839
116 140 1.634189134372689 0.000971887554356 1.000000000000000 0.000002130074799
117 141 1.634189134355517 0.001529784316358 1.000000000000000 0.000003291478863
118 142 1.634189134311859 0.002499449956559 1.000000000000000 0.000005112368714
119 143 1.634189134215200 0.003985061589924 1.000000000000000 0.000007586001966
120 144 1.634189134052264 0.005715536581952 1.000000000000000 0.000009770969678
121 145 1.634189133858041 0.006094225362163 1.000000000000000 0.000008661777969
122 146 1.634189133697537 0.004799333537357 1.000000000000000 0.000002522553667
123 147 1.634189133656614 0.004526928082046 1.000000000000000 0.000003218136913
124 148 1.634189133643932 0.001364480880998 1.000000000000000 0.000001555814389
125 149 1.634189133640638 0.001364480880998 1.000000000000000 0.000000138621888
Convergence criteria met.
After: gradient norm = 1.3862188842829628E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.3417,1.3417}
Count Table 1:
---------------
h: {-0.5639,0.5639}
Count Table 2:
---------------
h: {-0.3644,0.3644}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.9535}
Activity(exp=1): {0.0003,0.2722}
Activity(exp=2): {0.0004,0.0502}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): 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Dinucleotide(d=4): 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Dinucleotide(d=5): 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Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Suggested variations:
key=0;0;0, description = Initial model.
> Optimizing variation "Initial model." (component0-2-variation0).
>> Starting new optimization: component0-2-variation0. (2021-05-21 16:16:28.689).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5]]},{}]}
Value and gradient before optimization:
=======================================
value = 1.6341891336406378
gradient = {0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 1.3862188842806192E-7
Already at minimum!
After: gradient norm = 1.3862188842806192E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.3417,1.3417}
Count Table 1:
---------------
h: {-0.5639,0.5639}
Count Table 2:
---------------
h: {-0.3644,0.3644}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.9535}
Activity(exp=1): {0.0003,0.2722}
Activity(exp=2): {0.0004,0.0502}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): 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Dinucleotide(d=4): 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Dinucleotide(d=5): 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Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
The Likelihood DID improve.
> No varitions possible for Binding mode 0.
> Optimizing the full model (component0-4-all).
>> Starting new optimization: component0-4-all. (2021-05-21 16:16:29.164).
>>> Packing before optimization
Packing: {"enrichmentModel":[{"delta":[-1,-1]},{"delta":[-1,-1]},{"delta":[-1,-1]}],"countTable":[{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5]]},{}]}
Value and gradient before optimization:
=======================================
value = 1.6341891336406376
gradient = {0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 1.3862188842816176E-7
Already at minimum!
After: gradient norm = 1.3862188842816176E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.3417,1.3417}
Count Table 1:
---------------
h: {-0.5639,0.5639}
Count Table 2:
---------------
h: {-0.3644,0.3644}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.9535}
Activity(exp=1): {0.0003,0.2722}
Activity(exp=2): {0.0004,0.0502}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): 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Dinucleotide(d=4): 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Dinucleotide(d=5): 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Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
==================================
== Starts fiting Binding mode 1 ==
==================================
> Optimizing h (component1-0-h).
>> Starting new optimization: component1-0-h. (2021-05-21 16:16:30.441).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 1.6497333095193176
gradient = {-0.0427,0.0427,-0.0508,0.0508,-0.0093,0.0093}
gradient norm = 0.0948000341328404
Starting Function Value: 1.6497333095193176
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 1.635042253828130 0.290160573353551 3.060764439672650 0.034628804455941
2 4 1.632683783208216 0.113333542789725 1.000000000000000 0.010831539234507
3 5 1.632489748513137 0.040934292591663 1.000000000000000 0.001387657621406
4 6 1.632487559263592 0.004749138486698 1.000000000000000 0.000551342198848
5 7 1.632487217719017 0.001250946250380 1.000000000000000 0.000008416461782
6 8 1.632487217579324 0.000035796731800 1.000000000000000 0.000000520229071
7 9 1.632487217578979 0.000035796731800 1.000000000000000 0.000000019715813
Convergence criteria met.
After: gradient norm = 1.9715812996580653E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.1093,1.1093}
Count Table 1:
---------------
h: {-0.4380,0.4380}
Count Table 2:
---------------
h: {-0.3434,0.3434}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.9535}
Activity(exp=1): {0.0003,0.2722}
Activity(exp=2): {0.0004,0.0502}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): 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Dinucleotide(d=4): 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Dinucleotide(d=5): 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Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0864,1.0397}
Activity(exp=1): {0.0865,0.3583}
Activity(exp=2): {0.0865,0.1363}
> Initial optimization (component1-1-f1).
>> Starting new optimization: component1-1-f1. (2021-05-21 16:16:35.287).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[122,123]},{"h":[124,125]},{"h":[126,127]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119],"activity":[[120,121],[120,121],[120,121]]}]}
Value and gradient before optimization:
=======================================
value = 1.652592315560479
gradient = {-0.0001,-0.0001,-0.0001,-0.0005,0.0000,-0.0004,-0.0000,0.0001,0.0003,0.0004,-0.0001,-0.0001,-0.0001,-0.0003,0.0020,-0.0009,-0.0002,0.0003,0.0002,-0.0002,-0.0003,-0.0004,-0.0002,-0.0002,0.0001,-0.0006,-0.0001,0.0002,0.0005,0.0003,0.0002,-0.0001,-0.0008,-0.0002,0.0026,-0.0010,-0.0001,0.0001,-0.0000,-0.0001,0.0010,0.0001,-0.0001,-0.0006,0.0001,0.0017,0.0000,-0.0002,0.0003,-0.0011,0.0001,0.0000,-0.0002,0.0001,0.0011,0.0011,-0.0002,-0.0032,0.0004,-0.0001,-0.0005,0.0000,-0.0005,-0.0006,-0.0002,-0.0024,-0.0000,0.0006,0.0009,0.0005,-0.0001,0.0000,0.0006,-0.0000,0.0031,-0.0011,-0.0002,0.0005,-0.0005,-0.0001,-0.0001,0.0001,-0.0001,-0.0002,-0.0002,0.0004,0.0001,-0.0003,0.0003,-0.0007,-0.0005,0.0001,0.0000,-0.0000,0.0021,-0.0001,-0.0002,-0.0004,-0.0000,-0.0001,0.0008,0.0000,0.0001,0.0003,-0.0008,0.0001,0.0000,-0.0001,0.0001,-0.0009,-0.0000,0.0000,0.0003,0.0001,0.0006,0.0004,0.0001,-0.0003,-0.0005,-0.0002,0.0000,0.0002,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 0.007884557070544293
Starting Function Value: 1.652592315560479
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 1.648084668915588 1.000000000000000 126.83020632013350 0.030650964455018
2 3 1.640672574328487 10.143876222394962 1.000000000000000 0.047063222812547
3 4 1.635033511018392 1.077545368719622 1.000000000000000 0.021937725420552
4 5 1.634382784562537 1.297907614907698 1.000000000000000 0.024273327889012
5 6 1.633678084673345 0.117470008148960 1.000000000000000 0.003632321203332
6 7 1.633592549891505 0.256347389134987 1.000000000000000 0.002648505209220
7 8 1.633379979391764 1.752364686078098 1.000000000000000 0.003875075821365
8 10 1.633354377756059 0.033540941191449 0.082614575417429 0.003711340122372
9 11 1.633315767249872 0.326657224287931 1.000000000000000 0.002933495002698
10 12 1.633234061815065 0.095496853866413 1.000000000000000 0.003239391187924
11 13 1.632607615166114 0.661157071691206 1.000000000000000 0.009332210160876
12 14 1.632082516579321 0.667863237459936 1.000000000000000 0.010185741176582
13 15 1.631536593309677 1.428568493175451 1.000000000000000 0.008395381268891
14 16 1.630903496865747 1.016028951734807 1.000000000000000 0.003783935463461
15 17 1.630368746659237 0.876159865893991 1.000000000000000 0.005183025778527
16 18 1.630108833359154 0.307286187626459 1.000000000000000 0.005672759244340
17 19 1.629903776715112 0.422097814083528 1.000000000000000 0.001839356247411
18 20 1.629748988987896 0.602372266545039 1.000000000000000 0.004294343458681
19 21 1.629654804979642 0.441457647781453 1.000000000000000 0.006012010398347
20 22 1.629441738526327 0.833189538258158 1.000000000000000 0.007233843886285
21 23 1.629162494257875 0.852024808652862 1.000000000000000 0.005425124674014
22 24 1.628982614158824 0.700734710596887 1.000000000000000 0.001979988452126
23 25 1.628936489660047 0.441823500954910 1.000000000000000 0.000673929073154
24 26 1.628917333788307 0.430204659682724 1.000000000000000 0.001327915295418
25 27 1.628904657739736 0.106415311683276 1.000000000000000 0.001249660812025
26 28 1.628799002419598 0.488679302083405 1.000000000000000 0.001009270759869
27 29 1.628674240643690 0.456046042863724 1.000000000000000 0.001677877580570
28 30 1.628548877909588 0.789187973994630 1.000000000000000 0.001699727760984
29 31 1.628478442537797 0.704761424550989 1.000000000000000 0.000627204328600
30 32 1.628448547060146 0.516721647166311 1.000000000000000 0.000515088301099
31 33 1.628433595240725 0.226887573516868 1.000000000000000 0.000885066189753
32 34 1.628402148097027 0.363974915461507 1.000000000000000 0.001266935641474
33 35 1.628367753968564 0.350515318423848 1.000000000000000 0.001142363122332
34 36 1.628326093381625 0.412988053928491 1.000000000000000 0.000477260966310
35 37 1.628302357034704 0.412357701307797 1.000000000000000 0.000414885730500
36 38 1.628296841493278 0.093034621207105 1.000000000000000 0.000504818309528
37 39 1.628288991747567 0.137588455504647 1.000000000000000 0.000326876136880
38 40 1.628283986921278 0.172306341406790 1.000000000000000 0.000093287406180
39 41 1.628281419750192 0.156853683412372 1.000000000000000 0.000242408246746
40 42 1.628279674760145 0.098815428408062 1.000000000000000 0.000316118535509
41 43 1.628276823051952 0.100689604198104 1.000000000000000 0.000289666894678
42 44 1.628271993954848 0.148669744727753 1.000000000000000 0.000143851495511
43 45 1.628269955804131 0.136277873328648 1.000000000000000 0.000068123504366
44 46 1.628269421467603 0.047081221796625 1.000000000000000 0.000116605531378
45 47 1.628268621237685 0.051369509161477 1.000000000000000 0.000144278544531
46 48 1.628267514906884 0.072277271536263 1.000000000000000 0.000102583182660
47 49 1.628266506055173 0.114275677783894 1.000000000000000 0.000029715615077
48 50 1.628266158995815 0.061141233823368 1.000000000000000 0.000060598213948
49 51 1.628265904138934 0.038578339931184 1.000000000000000 0.000085097689977
50 52 1.628265561845104 0.031942465718366 1.000000000000000 0.000080475300303
51 53 1.628264879690481 0.072412511749266 1.000000000000000 0.000029055269136
52 54 1.628264647108262 0.050749935976536 1.000000000000000 0.000012533275022
53 55 1.628264582454585 0.012689146099680 1.000000000000000 0.000019478031396
54 56 1.628264473545751 0.022236959503230 1.000000000000000 0.000017804152465
55 57 1.628264338486831 0.030711321561295 1.000000000000000 0.000027753042728
56 58 1.628264288784875 0.022136635882619 1.000000000000000 0.000009269662850
57 59 1.628264276416825 0.010219084158566 1.000000000000000 0.000008156693212
58 60 1.628264258600080 0.008429505667368 1.000000000000000 0.000010284009421
59 61 1.628264234024284 0.013591715908807 1.000000000000000 0.000006224074039
60 62 1.628264222822528 0.008001536755166 1.000000000000000 0.000005014542983
61 63 1.628264206657993 0.013895314192281 1.000000000000000 0.000006598466564
62 64 1.628264200861354 0.007274555957394 1.000000000000000 0.000006319145914
63 65 1.628264193302357 0.007412301157068 1.000000000000000 0.000002972297262
64 66 1.628264187980581 0.009253825649922 1.000000000000000 0.000002552874380
65 67 1.628264186707982 0.001959164194531 1.000000000000000 0.000002769206835
66 68 1.628264181195765 0.008689351610556 1.000000000000000 0.000003932796686
67 69 1.628264178349987 0.006917412802093 1.000000000000000 0.000001870358374
68 70 1.628264177080483 0.003327854312118 1.000000000000000 0.000001613481183
69 71 1.628264175624827 0.003610167063903 1.000000000000000 0.000002055638675
70 72 1.628264173669739 0.004437862063203 1.000000000000000 0.000002472790056
71 73 1.628264169172045 0.010562500371237 1.000000000000000 0.000002855828522
72 74 1.628264162740024 0.017016302268785 1.000000000000000 0.000003308327850
73 75 1.628264156827185 0.019155723105852 1.000000000000000 0.000003160698788
74 76 1.628264152365956 0.012600129085524 1.000000000000000 0.000002971561106
75 77 1.628264142282438 0.027832647317405 1.000000000000000 0.000005153623259
76 78 1.628264133598516 0.030702109663110 1.000000000000000 0.000004776710071
77 79 1.628264126645918 0.020588605185039 1.000000000000000 0.000003141932132
78 80 1.628264119702626 0.024701034746312 1.000000000000000 0.000001695126558
79 81 1.628264117481415 0.006914208060785 1.000000000000000 0.000001773895562
80 82 1.628264115518354 0.006891007121905 1.000000000000000 0.000002304891738
81 83 1.628264114000142 0.005258013873734 1.000000000000000 0.000001778042338
82 84 1.628264112029743 0.005258013873734 1.000000000000000 0.000001027941806
Convergence criteria met.
After: gradient norm = 1.0279418062852506E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.0965,1.0965}
Count Table 1:
---------------
h: {-0.4566,0.4566}
Count Table 2:
---------------
h: {-0.3475,0.3475}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.9535}
Activity(exp=1): {0.0003,0.2722}
Activity(exp=2): {0.0004,0.0502}
Binding mode 1:
---------------
Mononucleotide: {0.2364,0.6435,0.8945,1.4339,-0.0502,0.2210,0.5233,-0.7887,-1.0191,-0.8226,-0.0113,0.3146,-0.1810,0.7211,-1.4385,0.5571,0.0680,-0.9651,-0.2805,0.5659,0.6706,1.2869,1.1573,0.7880,-0.7852,0.8820,0.1469,-1.1610,-1.6037,-0.5578,-0.2252,0.6576,0.6949,0.2511,-1.7601,0.7757,0.0018,-0.7392,-0.0711,0.2128,-0.2749,-0.4276,1.1679,1.6704,-0.2182,-2.1648,0.1875,1.4254,-2.2790,1.3418,0.3998,0.2510,1.2432,-0.3804,-3.4583,-1.4284,1.3549,1.9874,-0.5771,0.8015,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.8583,-0.0044,1.4761,1.6220,0.9493,1.8499,0.3753,-1.2889,-2.3233,-1.1462,0.4436,0.2787,-4.2072,0.6643,-2.2265,1.1993,0.3221,-0.7058,1.5677,0.9180,0.2372,-0.1866,0.4511,0.5754,0.5355,-0.4460,-0.7878,0.5758,-1.7213,0.6613,1.0982,-0.2446,-0.0287,0.0951,-2.0635,0.2322,0.4554,0.4872,0.3669,0.3295,-0.6560,0.0156,0.2604,-0.1108,1.7665,0.0347,-0.0710,0.2565,-1.3555,0.7940,0.2122,0.0320,-0.5016,-0.7667,-1.4008,-0.5429,-0.4006,0.2708,1.6438,1.1417}
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Dinucleotide(d=4): 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Dinucleotide(d=5): 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Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-0.0275,0.2393}
Activity(exp=1): {-0.0275,0.2393}
Activity(exp=2): {-0.0275,0.2393}
Suggested variations:
key=7;3;0, description = Initial model.
> Optimizing variation "Initial model." (component1-2-variation0).
>> Starting new optimization: component1-2-variation0. (2021-05-21 16:17:31.081).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[122,123]},{"h":[124,125]},{"h":[126,127]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119],"activity":[[120,121],[120,121],[120,121]]}]}
Value and gradient before optimization:
=======================================
value = 1.6282641120297432
gradient = {-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 1.0279418062855617E-6
Already at minimum!
After: gradient norm = 1.0279418062855617E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.0965,1.0965}
Count Table 1:
---------------
h: {-0.4566,0.4566}
Count Table 2:
---------------
h: {-0.3475,0.3475}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.9535}
Activity(exp=1): {0.0003,0.2722}
Activity(exp=2): {0.0004,0.0502}
Binding mode 1:
---------------
Mononucleotide: {0.2364,0.6435,0.8945,1.4339,-0.0502,0.2210,0.5233,-0.7887,-1.0191,-0.8226,-0.0113,0.3146,-0.1810,0.7211,-1.4385,0.5571,0.0680,-0.9651,-0.2805,0.5659,0.6706,1.2869,1.1573,0.7880,-0.7852,0.8820,0.1469,-1.1610,-1.6037,-0.5578,-0.2252,0.6576,0.6949,0.2511,-1.7601,0.7757,0.0018,-0.7392,-0.0711,0.2128,-0.2749,-0.4276,1.1679,1.6704,-0.2182,-2.1648,0.1875,1.4254,-2.2790,1.3418,0.3998,0.2510,1.2432,-0.3804,-3.4583,-1.4284,1.3549,1.9874,-0.5771,0.8015,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.8583,-0.0044,1.4761,1.6220,0.9493,1.8499,0.3753,-1.2889,-2.3233,-1.1462,0.4436,0.2787,-4.2072,0.6643,-2.2265,1.1993,0.3221,-0.7058,1.5677,0.9180,0.2372,-0.1866,0.4511,0.5754,0.5355,-0.4460,-0.7878,0.5758,-1.7213,0.6613,1.0982,-0.2446,-0.0287,0.0951,-2.0635,0.2322,0.4554,0.4872,0.3669,0.3295,-0.6560,0.0156,0.2604,-0.1108,1.7665,0.0347,-0.0710,0.2565,-1.3555,0.7940,0.2122,0.0320,-0.5016,-0.7667,-1.4008,-0.5429,-0.4006,0.2708,1.6438,1.1417}
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Dinucleotide(d=4): 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Dinucleotide(d=5): 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Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-0.0275,0.2393}
Activity(exp=1): {-0.0275,0.2393}
Activity(exp=2): {-0.0275,0.2393}
The Likelihood DID NOT improve. Discarding fit component1-2-variation0.
> No varitions possible for Binding mode 1.
> Unfreezing component (component1-3-f0).
>> Starting new optimization: component1-3-f0. (2021-05-21 16:17:32.251).
>>> Packing before optimization
Packing: 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Value and gradient before optimization:
=======================================
value = 3.4696581498913295
gradient = 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gradient norm = 6.814813072153819E-4
Starting Function Value: 3.4696581498913295
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 3.469047914705276 1.000000000000003 1467.3916795841774 0.000649130466253
2 4 3.469029195924439 0.057834778407842 0.007094489749666 0.002975177277279
3 5 3.467911531094271 3.788734910715880 1.000000000000000 0.001314255223748
4 7 3.467906481346781 0.030337389565523 0.020392774409348 0.001242609100002
5 8 3.467880228892489 0.587680112087773 1.000000000000000 0.000772697054560
6 9 3.467835871637687 0.201968601444932 1.000000000000000 0.001110836190636
7 11 3.467795116529914 0.270438785453990 0.294591345702655 0.003513484428337
8 12 3.467760534126951 0.179541774629613 1.000000000000000 0.000914609021589
9 13 3.467756225120781 0.010860381294879 1.000000000000000 0.000830709679792
10 14 3.467710943182647 0.079959148197715 1.000000000000000 0.001494409041744
11 15 3.467648572014904 0.214256746608132 1.000000000000000 0.002388158014764
12 16 3.467574563948856 0.443134262652566 1.000000000000000 0.002189992279599
13 17 3.467489354770347 0.539040138022007 1.000000000000000 0.000963988519295
14 18 3.467392162267377 0.760265469294806 1.000000000000000 0.001626054805452
15 19 3.467345306021897 0.285091376396208 1.000000000000000 0.002343317446590
16 20 3.467273195692512 0.488899139506484 1.000000000000000 0.002099265055028
17 21 3.467184752150957 0.505224479562384 1.000000000000000 0.001093954897167
18 22 3.467124304151266 0.575621050638185 1.000000000000000 0.000551489562745
19 23 3.467118740800938 0.042537742733283 1.000000000000000 0.000454098296885
20 24 3.467098085632862 0.152671735590309 1.000000000000000 0.000372766420548
21 25 3.467076804670040 0.222040147452958 1.000000000000000 0.000908351456015
22 26 3.467055979214223 0.271821244345125 1.000000000000000 0.001123653467085
23 27 3.467034703923261 0.266637837973607 1.000000000000000 0.000651016293472
24 28 3.467021164648880 0.207019197106183 1.000000000000000 0.000282867433991
25 29 3.467015210144750 0.081329741843321 1.000000000000000 0.000656624719539
26 30 3.467006215317113 0.115225574088246 1.000000000000000 0.001062100265581
27 31 3.466992970913648 0.187975318880645 1.000000000000000 0.001227779281432
28 32 3.466975310322343 0.275213600359731 1.000000000000000 0.000829022562372
29 33 3.466962786991340 0.247294458578640 1.000000000000000 0.000190543552896
30 34 3.466958590486096 0.075351408849263 1.000000000000000 0.000511299326299
31 35 3.466954455318590 0.060186907006049 1.000000000000000 0.000821282066516
32 36 3.466947489125827 0.105409424902092 1.000000000000000 0.001038059822922
33 37 3.466937335043866 0.188421956045051 1.000000000000000 0.000913798851635
34 38 3.466927334496891 0.217120282609393 1.000000000000000 0.000405806074719
35 39 3.466922642340726 0.142160367550034 1.000000000000000 0.000233898757906
36 40 3.466921186678062 0.034069880839277 1.000000000000000 0.000404121363912
37 41 3.466918638248135 0.057271510796511 1.000000000000000 0.000543780315415
38 42 3.466915396385153 0.082368872706868 1.000000000000000 0.000487394886304
39 43 3.466910355549310 0.135828635823186 1.000000000000000 0.000256993835154
40 44 3.466906223902332 0.157371031944560 1.000000000000000 0.000185038619778
41 45 3.466904649488382 0.058464451145823 1.000000000000000 0.000321091573195
42 46 3.466902663205915 0.072140277092890 1.000000000000000 0.000360239920231
43 47 3.466899196153590 0.110941232709639 1.000000000000000 0.000247133235953
44 48 3.466894986498170 0.191873205658506 1.000000000000000 0.000119164945778
45 49 3.466893943229882 0.053645096586776 1.000000000000000 0.000211313079965
46 50 3.466892955107085 0.049894174635417 1.000000000000000 0.000216599474254
47 51 3.466890551152365 0.108126740919151 1.000000000000000 0.000105955715931
48 52 3.466888982760343 0.115513896971272 1.000000000000000 0.000080100927218
49 53 3.466888741163145 0.018053499502958 1.000000000000000 0.000086421938972
50 54 3.466887360323506 0.080464483922755 1.000000000000000 0.000067327196799
51 55 3.466885678842687 0.142906066463985 1.000000000000000 0.000032732252412
52 56 3.466884967804512 0.081287572025794 1.000000000000000 0.000040431973400
53 57 3.466884541870699 0.065014361580952 1.000000000000000 0.000030006575098
54 58 3.466884151515107 0.057060688476511 1.000000000000000 0.000071588815332
55 59 3.466883861298355 0.046750091370334 1.000000000000000 0.000030923010060
56 60 3.466883748968570 0.018017971290860 1.000000000000000 0.000016422548012
57 61 3.466883644530868 0.018651144261343 1.000000000000000 0.000024960348512
58 62 3.466883544836415 0.020360664733730 1.000000000000000 0.000029283472722
59 63 3.466883383545745 0.032929293176353 1.000000000000000 0.000020781214173
60 64 3.466883227373946 0.041118505752102 1.000000000000000 0.000009272468644
61 65 3.466883153938890 0.023204269130658 1.000000000000000 0.000010489639010
62 66 3.466883095341664 0.020291786602528 1.000000000000000 0.000012761915267
63 67 3.466883020176658 0.025909116370980 1.000000000000000 0.000011603717226
64 68 3.466882938759928 0.044360551444551 1.000000000000000 0.000008223029083
65 69 3.466882916510258 0.009811810067452 1.000000000000000 0.000004883456892
66 70 3.466882901074652 0.008999785638338 1.000000000000000 0.000003845299124
67 71 3.466882885496657 0.011933216464264 1.000000000000000 0.000002996956456
68 72 3.466882871582476 0.015592727564939 1.000000000000000 0.000002570063567
69 73 3.466882859461509 0.015554224382596 1.000000000000000 0.000005885279126
70 74 3.466882855736558 0.006194075162352 1.000000000000000 0.000002213208004
71 75 3.466882854538634 0.002470858982224 1.000000000000000 0.000001565846064
72 76 3.466882853574892 0.001886946906256 1.000000000000000 0.000002396411305
73 77 3.466882852072379 0.002942852727596 1.000000000000000 0.000003027894043
74 78 3.466882850060341 0.004338662732817 1.000000000000000 0.000002537055157
75 79 3.466882847883007 0.004338662732817 1.000000000000000 0.000001166179546
Convergence criteria met.
After: gradient norm = 1.1661795460639771E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.0917,1.0917}
Count Table 1:
---------------
h: {-0.4567,0.4567}
Count Table 2:
---------------
h: {-0.3475,0.3475}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.9535}
Activity(exp=1): {0.0003,0.2722}
Activity(exp=2): {0.0004,0.0502}
Binding mode 1:
---------------
Mononucleotide: {0.1507,0.4305,0.7092,0.9834,-0.0926,0.1154,0.3245,-0.5617,-0.6611,-0.4494,0.0220,0.2617,-0.1271,0.4687,-0.9058,0.3050,-0.0032,-0.6638,-0.0687,0.3074,0.4322,0.9073,0.8479,0.5145,-0.5282,0.5861,0.0658,-0.7741,-1.1106,-0.3927,-0.1532,0.4943,0.3946,0.1734,-1.1096,0.4541,0.0463,-0.4583,0.0476,0.1079,-0.0042,-0.3474,0.8056,1.0798,-0.1705,-1.4766,0.0626,1.0689,-1.6933,1.0192,0.2705,0.0420,0.9061,-0.0556,-2.5941,-0.9231,0.9540,1.3916,-0.3051,0.5148,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.5579,-0.0053,0.9372,1.0354,0.6491,1.1636,0.2760,-0.6961,-1.6995,-0.5553,0.4221,0.2589,-3.1209,0.4186,-1.5065,0.7656,0.3032,-0.3426,1.0427,0.6412,0.1983,-0.0608,0.2497,0.3705,0.4390,-0.3282,-0.6013,0.4220,-1.3114,0.5991,0.7703,-0.1251,-0.0005,0.0745,-1.4935,0.1832,0.3252,0.3596,0.2736,0.2009,-0.4351,-0.0407,0.1054,-0.0739,1.1653,0.0298,-0.0771,0.2372,-1.0634,0.5489,0.1856,-0.0956,-0.2637,-0.4294,-0.9809,-0.2705,-0.2260,0.3290,1.0700,0.8303}
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Dinucleotide(d=6): {-0.1048,0.0169,0.0043,0.1557,0.1089,-0.0049,0.0019,0.0106,-0.0413,-0.0201,0.0068,-0.0251,-0.1014,0.0501,-0.0361,-0.0968,-0.0375,0.0663,0.0509,0.0636,0.0573,0.0481,0.0431,-0.0257,0.0666,0.0007,-0.0022,0.0144,-0.0121,-0.0423,0.0237,-0.0193,0.0067,-0.0146,-0.0139,0.0895,-0.0027,0.1138,0.0558,0.0284,0.1213,0.0132,-0.0027,-0.0142,0.0183,-0.0179,0.0159,0.0443,-0.0002,0.1844,0.0154,0.0234,0.1283,-0.0401,0.0213,0.0738,0.0556,0.0989,0.0174,0.0583,0.1949,0.0204,0.0098,-0.0414,0.0553,0.1453,0.0014,0.0285,-0.0254,0.0575,0.0466,0.0047,0.0336,0.0551,0.1279,0.1809,0.0662,0.1814,0.1259,0.0505,-0.0768,-0.0201,0.0801,0.0203,-0.0385,0.0187,0.0361,0.0381,-0.0263,0.0132,0.0220,0.0083,0.0239,0.0504,0.0047,0.0890,-0.0694,-0.2580,-0.0695,-0.0061,-0.0681,-0.0144,0.0363,-0.0358,0.0371,-0.0113,-0.0213,0.0033,-0.0641,0.0555,-0.0060,-0.0482,0.0962,0.1301,-0.0452,-0.1390,-0.0649,-0.0348,0.1514,0.0694,0.0550,0.0062,-0.0148,0.0326,0.0315,0.0403,0.0117,0.0045,0.0199,-0.0140,0.0036,0.0031,0.0769,-0.0434,0.0591,0.0357,-0.0117,-0.0142,-0.0156,0.0244,-0.0185,-0.0426,-0.0210,0.0087,-0.0270,-0.0398,0.0191,-0.0103,0.0122,-0.0799,0.0028,-0.0155,-0.0457,-0.0355,-0.0905,-0.0091,-0.0231,-0.0139,-0.0077,0.0062,-0.0311,0.0171,-0.0646,-0.2698,0.1168,-0.1858,-0.0450,-0.0186,-0.0187,0.1188,0.0080,-0.0046,-0.1057,-0.0646,-0.0697,0.0301,-0.0242,0.0408,0.0256,0.0000,-0.1398,-0.0578,-0.0088,0.1244,-0.0010,-0.0365,-0.0656,0.0314,-0.0335,-0.2201,-0.0605,-0.0711,0.0673,0.0098,0.0235,-0.0478,-0.0242,-0.2591,0.2172,0.0875,0.0301,-0.0454,0.0080,0.1293,0.1255,0.0922,-0.0271,-0.0097,0.0148,-0.1868,-0.0331,-0.0087,-0.0537,-0.0841,0.0011,-0.0927,-0.0033,-0.0998,0.1439,0.0241,-0.0049,0.0189,-0.0001,-0.0247,0.0713,0.0260,0.0101,0.0040,0.0154,0.0266,0.0057,0.0057,-0.0444,0.0208,0.0446,0.0353,0.0012,-0.0277,0.0047,0.0321,-0.0458,0.1024,-0.0294,-0.2174,0.1646,-0.0776,-0.0098,-0.0088,-0.0431,0.0112,-0.0763,0.0205,-0.0344,-0.0525,-0.2020,-0.0378,0.0860,0.1076,0.1194,-0.0002,0.0956,0.0225,-0.0573,-0.0146,-0.0037,-0.0399,-0.0231,-0.0294,-0.0423,0.1178,-0.0358,-0.0123,0.1217,0.0375,0.0999,-0.0531,0.0783,0.1538,0.0339,-0.0082,-0.1567,-0.1166,-0.1292,-0.0456,0.2640,-0.2749,-0.0808,-0.0941,-0.0931,0.1909,0.0491,-0.0586,-0.1996,-0.2401,-0.4557,-0.0515,-0.2211,0.2832,0.2248,0.2516,-0.1060,0.0182,-0.0826,-0.0958,0.2661,0.0965,-0.0833,0.1334,-0.1443,0.1594,0.0152,0.0025,-0.1289,-0.1899,-0.1019,-0.1267,0.1063,0.1371,0.1686,0.0786,0.0329,-0.1305,0.0579,-0.3018,0.3057,-0.0952,0.0226,0.0947,-0.1069,0.1879,0.1277,0.0009,-0.1427,-0.1305,0.0016,-0.1871,-0.1518,-0.0732,0.1557,0.0965,-0.1890,0.0410,0.0682,-0.0316,0.0364,-0.1326,0.0706,-0.0600,-0.0340,0.0212,0.0364,-0.0223,-0.0482,0.0337,-0.1339,-0.1207,-0.0449,-0.0612,-0.0466,0.0887,-0.1311,-0.0430,0.0625,0.3226,-0.0455,0.2004,0.0021,-0.0629,-0.0636,-0.2127,-0.0771,0.0456,-0.0056,0.0645,-0.0084,0.0638,-0.0346,-0.3174,0.0081,-0.0216,0.0124,0.0068,0.0282,0.0034,0.0005,0.1285,0.0120,0.0059,0.0098,0.0113,-0.0030,0.0086,0.0067,-0.0053,0.0118,0.0047,0.0160,0.0105,0.0008,0.0016}
Activity(exp=0): {-0.0084,0.1716}
Activity(exp=1): {-0.0084,0.1716}
Activity(exp=2): {-0.0084,0.1716}
> Optimizing the full model (component1-4-all).
>> Starting new optimization: component1-4-all. (2021-05-21 16:22:13.991).
>>> Packing before optimization
Packing: 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Value and gradient before optimization:
=======================================
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gradient norm = 0.02023119376708661
Starting Function Value: 3.466882847883007
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 3.452129750435787 0.999999999999994 49.428620550650024 0.046554049619879
2 3 3.441555788287271 2.039449191275285 1.000000000000000 0.036891560898088
3 5 3.439430065941849 0.127896837396311 0.239693120147489 0.024321087882727
4 6 3.436965159042940 0.570875829629529 1.000000000000000 0.007097945342948
5 7 3.436573935896132 0.058060266425492 1.000000000000000 0.007216799965484
6 9 3.434061570971741 0.402638936258872 0.026691201230241 0.019986286640882
7 11 3.432222474565533 0.438268735114132 0.189692224429168 0.038009957965548
8 12 3.431145555225912 0.397495615736076 1.000000000000000 0.044211831691109
9 13 3.429840176802989 0.142103575184856 1.000000000000000 0.036174163453358
10 14 3.427262448897883 0.461452412993279 1.000000000000000 0.011839925685696
11 15 3.427130287343385 0.094835491582718 1.000000000000000 0.005338389029488
12 16 3.427071458884157 0.015831029929227 1.000000000000000 0.004559351039920
13 17 3.426521021349114 0.231666797429453 1.000000000000000 0.005673284781763
14 18 3.426252374523619 0.217304968002821 1.000000000000000 0.005152838698197
15 19 3.425587962614138 0.444109288369122 1.000000000000000 0.005164411917453
16 20 3.424374266011509 1.431575304018687 1.000000000000000 0.006682065120198
17 21 3.423428663066138 0.220160380626270 1.000000000000000 0.006139748420017
18 22 3.422032895994944 0.947328566871666 1.000000000000000 0.006897117030441
19 23 3.421412172794450 0.346949739571233 1.000000000000000 0.004762793268458
20 24 3.420657006763938 1.346598306163060 1.000000000000000 0.011916887580184
21 25 3.420154528461883 0.393104990379482 1.000000000000000 0.006802239525856
22 26 3.419795842568461 0.184996209506875 1.000000000000000 0.002588072929906
23 27 3.419541918174044 0.313217505000220 1.000000000000000 0.006050950630388
24 28 3.419334401718170 0.294326062562575 1.000000000000000 0.006856056811305
25 29 3.418921530528275 0.434383944840776 1.000000000000000 0.005591979631115
26 30 3.418383827788428 0.610056679039851 1.000000000000000 0.003116162000414
27 31 3.417986127392150 0.474455421251656 1.000000000000000 0.002411980423302
28 32 3.417667838075916 0.393991085267597 1.000000000000000 0.003725105414361
29 33 3.417441257058580 0.373192979224082 1.000000000000000 0.002251927581849
30 34 3.417298315987110 0.230500534981998 1.000000000000000 0.002929142364412
31 35 3.417146674084192 0.258854359070092 1.000000000000000 0.001943761538115
32 36 3.417022003302908 0.221384725875289 1.000000000000000 0.002307744458009
33 37 3.416825756720823 0.345478576942935 1.000000000000000 0.002295834183786
34 38 3.416545393694091 0.632463311880701 1.000000000000000 0.001535947770502
35 39 3.416373244672264 0.530077229879875 1.000000000000000 0.001765227150599
36 40 3.416234807341681 0.317404629161767 1.000000000000000 0.001329391794672
37 41 3.416136105523039 0.273353682849008 1.000000000000000 0.001440396008007
38 42 3.416029438605433 0.337588765647711 1.000000000000000 0.001199900772367
39 43 3.415911679336933 0.699138227299036 1.000000000000000 0.002010556194759
40 44 3.415835050869853 0.150018921241977 1.000000000000000 0.001372351309765
41 45 3.415767376209113 0.255524080756769 1.000000000000000 0.000779010008436
42 46 3.415727528897999 0.178393849732221 1.000000000000000 0.000702291442914
43 47 3.415656332332512 0.374044319938747 1.000000000000000 0.000775581271127
44 48 3.415585729393294 0.404112097410871 1.000000000000000 0.001005516459721
45 49 3.415532332938930 0.515736400416412 1.000000000000000 0.000825744352004
46 50 3.415497616431540 0.146457328891420 1.000000000000000 0.000481247023105
47 51 3.415473928662789 0.106095890124319 1.000000000000000 0.000468617039559
48 52 3.415441027748599 0.223054236560050 1.000000000000000 0.000675224452081
49 53 3.415416096408206 0.324813432977974 1.000000000000000 0.000847979875916
50 54 3.415394373109312 0.167396081735232 1.000000000000000 0.000422755671010
51 55 3.415380269395739 0.142320834112135 1.000000000000000 0.000339472490192
52 56 3.415368398730635 0.116353744016278 1.000000000000000 0.000428388080057
53 57 3.415350769785484 0.201757396417429 1.000000000000000 0.000461794419356
54 58 3.415334230190467 0.221927373323971 1.000000000000000 0.000490826680431
55 59 3.415320297798189 0.227679596908329 1.000000000000000 0.000276118341516
56 60 3.415312449543970 0.076152041674425 1.000000000000000 0.000252956365234
57 61 3.415304450949209 0.094231845636834 1.000000000000000 0.000322648508196
58 62 3.415297216530844 0.137918704040299 1.000000000000000 0.000396359683168
59 63 3.415289484463114 0.142741689645202 1.000000000000000 0.000212498660897
60 64 3.415284595972966 0.095714127597430 1.000000000000000 0.000185269856004
61 65 3.415280257625776 0.093970696372415 1.000000000000000 0.000245647224695
62 66 3.415275018392519 0.111004907331219 1.000000000000000 0.000234082612438
63 67 3.415268879628441 0.173405259245594 1.000000000000000 0.000207336042586
64 68 3.415265958342920 0.146083832860405 1.000000000000000 0.000225934531539
65 69 3.415263463704885 0.028775436685310 1.000000000000000 0.000128821591699
66 70 3.415261516302993 0.035100694358573 1.000000000000000 0.000120742805117
67 71 3.415259456588208 0.061740351285581 1.000000000000000 0.000109956441370
68 72 3.415256668751151 0.120329988613471 1.000000000000000 0.000138637370849
69 73 3.415254988374747 0.131970528114885 1.000000000000000 0.000125993326936
70 74 3.415253778637170 0.029026418259862 1.000000000000000 0.000085439547255
71 75 3.415252644531504 0.037291283745693 1.000000000000000 0.000076265294657
72 76 3.415251616967048 0.043744398465582 1.000000000000000 0.000075226338269
73 77 3.415250630557870 0.104380232221563 1.000000000000000 0.000159267719195
74 78 3.415249512033646 0.042889700839215 1.000000000000000 0.000069196794182
75 79 3.415249145529617 0.012114703394742 1.000000000000000 0.000049467918855
76 80 3.415248566363905 0.034950333903977 1.000000000000000 0.000049640841644
77 81 3.415247886786089 0.045886714709137 1.000000000000000 0.000053005081972
78 82 3.415247140598465 0.082056435029179 1.000000000000000 0.000069243175794
79 83 3.415246982961390 0.057497175726420 1.000000000000000 0.000097815600456
80 84 3.415246679759104 0.016331241646900 1.000000000000000 0.000035558643032
81 85 3.415246517894697 0.008111615837811 1.000000000000000 0.000029391504701
82 86 3.415246274370403 0.020855671412574 1.000000000000000 0.000034703699729
83 87 3.415245955117707 0.035929613416287 1.000000000000000 0.000039395540630
84 88 3.415245673645965 0.061141899150983 1.000000000000000 0.000074926681405
85 89 3.415245532930067 0.015412306751416 1.000000000000000 0.000032682794831
86 90 3.415245458411055 0.009844775631438 1.000000000000000 0.000025436866542
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89 93 3.415245184183269 0.026163912938296 1.000000000000000 0.000054414225366
90 94 3.415245104613251 0.007978241436283 1.000000000000000 0.000023981129682
91 95 3.415245054841036 0.008779240767257 1.000000000000000 0.000016758437616
92 96 3.415245017223751 0.008073241559933 1.000000000000000 0.000017247014418
93 97 3.415244938239260 0.018816949105681 1.000000000000000 0.000017231357744
94 99 3.415244906754034 0.011220214495370 0.360809222221583 0.000026148674925
95 100 3.415244863748705 0.011166485246158 1.000000000000000 0.000013178214502
96 101 3.415244836063653 0.007310630939731 1.000000000000000 0.000010772652459
97 102 3.415244802908218 0.009306722387452 1.000000000000000 0.000012671209057
98 103 3.415244772100320 0.014699931922973 1.000000000000000 0.000018457581725
99 104 3.415244748060915 0.008366905120411 1.000000000000000 0.000009489176064
100 105 3.415244735119616 0.002772615305492 1.000000000000000 0.000007631863770
101 106 3.415244716160396 0.007071529463630 1.000000000000000 0.000010043904239
102 107 3.415244704713828 0.007837920818468 1.000000000000000 0.000011873240753
103 108 3.415244693819703 0.004150387388192 1.000000000000000 0.000008107798671
104 110 3.415244691071544 0.002014325893474 0.235295135882411 0.000034473150071
105 111 3.415244683294204 0.005440161109771 1.000000000000000 0.000008873498452
106 112 3.415244681361773 0.000977978475799 1.000000000000000 0.000006968088737
107 113 3.415244675102376 0.003761865424018 1.000000000000000 0.000006640313982
108 114 3.415244670689575 0.002373072388112 1.000000000000000 0.000006001910571
109 115 3.415244664775236 0.006761230476421 1.000000000000000 0.000042089910219
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111 117 3.415244658790595 0.000786607253834 1.000000000000000 0.000007687643205
112 118 3.415244657249189 0.001424702624627 1.000000000000000 0.000007080641533
113 119 3.415244653396079 0.002662655232053 1.000000000000000 0.000005968013205
114 121 3.415244651730761 0.002678449156748 0.195116591543304 0.000016543097882
115 122 3.415244647366328 0.003718499089048 1.000000000000000 0.000005680660001
116 123 3.415244646301783 0.000935227014217 1.000000000000000 0.000004563653994
117 124 3.415244644063963 0.001680488250463 1.000000000000000 0.000006222256699
118 125 3.415244642076309 0.002149816930703 1.000000000000000 0.000005028397558
119 126 3.415244639291035 0.002964494646197 1.000000000000000 0.000007740288432
120 127 3.415244637660577 0.002347497205846 1.000000000000000 0.000005145573526
121 128 3.415244636689852 0.001211299302568 1.000000000000000 0.000004546620506
122 129 3.415244635563340 0.001243749086916 1.000000000000000 0.000012034357944
123 130 3.415244634223625 0.001354965831538 1.000000000000000 0.000009592011605
124 131 3.415244632645134 0.001983115426899 1.000000000000000 0.000004270649998
125 132 3.415244631756313 0.001422139815303 1.000000000000000 0.000004189086655
126 133 3.415244631403609 0.002024940064514 1.000000000000000 0.000013548507142
127 134 3.415244630692071 0.000677797624627 1.000000000000000 0.000006267940333
128 135 3.415244630051164 0.000569137601805 1.000000000000000 0.000003050488060
129 136 3.415244629504461 0.000765885529159 1.000000000000000 0.000005220750597
130 137 3.415244628929655 0.001092724707285 1.000000000000000 0.000005371348504
131 138 3.415244627328382 0.002320191142253 1.000000000000000 0.000006812443966
132 139 3.415244626479459 0.003192387313936 1.000000000000000 0.000013563073224
133 140 3.415244625615662 0.000760618943142 1.000000000000000 0.000004262702069
134 141 3.415244625329959 0.000270534345407 1.000000000000000 0.000002987146260
135 142 3.415244624795164 0.000705934085216 1.000000000000000 0.000002469892192
136 143 3.415244623989738 0.001085421667258 1.000000000000000 0.000003075301934
137 145 3.415244623576151 0.001875320797565 0.424763074683473 0.000003590629949
138 146 3.415244622760893 0.001632114443342 1.000000000000000 0.000002915401313
139 147 3.415244622095130 0.000891262570980 1.000000000000000 0.000002454171821
140 148 3.415244621182271 0.002339400330894 1.000000000000000 0.000002863987789
141 149 3.415244620828028 0.001673258069955 1.000000000000000 0.000006188792266
142 150 3.415244620363277 0.000521733317808 1.000000000000000 0.000002797616152
143 151 3.415244619985488 0.000715164769125 1.000000000000000 0.000002141697676
144 152 3.415244619702498 0.000740056719870 1.000000000000000 0.000002732317856
145 153 3.415244619165711 0.001378188385264 1.000000000000000 0.000002834556543
146 154 3.415244618302863 0.002383398694702 1.000000000000000 0.000002397068919
147 156 3.415244617836001 0.001511972721341 0.451523165907335 0.000004120763891
148 157 3.415244617240732 0.001796117873685 1.000000000000000 0.000001782076931
149 158 3.415244616945557 0.000996555093286 1.000000000000000 0.000001681850243
150 159 3.415244616611097 0.000875403459619 1.000000000000000 0.000002371583599
151 160 3.415244616166859 0.001958058853074 1.000000000000000 0.000002125515485
152 161 3.415244615738683 0.001291200050811 1.000000000000000 0.000002018196789
153 162 3.415244615333302 0.001427211569160 1.000000000000000 0.000001688773219
154 163 3.415244615023634 0.001311851065008 1.000000000000000 0.000002329820817
155 164 3.415244614640363 0.001023492628627 1.000000000000000 0.000001525598441
156 165 3.415244614184651 0.001675427682080 1.000000000000000 0.000001588793211
157 166 3.415244613893806 0.001280071779086 1.000000000000000 0.000001916258489
158 167 3.415244613587682 0.002459558490229 1.000000000000000 0.000002872661516
159 168 3.415244613223107 0.002459558490229 1.000000000000000 0.000001334335616
Convergence criteria met.
After: gradient norm = 1.3343356161375619E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.5336,1.5336}
Count Table 1:
---------------
h: {-0.6410,0.6410}
Count Table 2:
---------------
h: {-0.4381,0.4381}
Enrichment model0:
--------------------
delta: {0.0000,-15.0000}
Enrichment model1:
--------------------
delta: {0.0000,-15.0000}
Enrichment model2:
--------------------
delta: {0.0000,-15.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0002,-2.4643}
Activity(exp=1): {0.0002,-2.0236}
Activity(exp=2): {0.0003,-2.8768}
Binding mode 1:
---------------
Mononucleotide: {0.0740,0.2686,0.5084,0.6236,-0.0131,-0.0294,0.2000,-0.2600,-0.2861,-0.1765,0.0061,0.2655,-0.1129,0.1607,-0.4438,0.1205,-0.0079,-0.2912,-0.0764,-0.3233,0.2457,0.4939,0.6699,0.2052,-0.1551,0.2881,0.0935,-0.3721,-0.5033,-0.2078,-0.0914,0.3306,0.1397,0.0735,-0.5442,0.1686,-0.0008,-0.2997,0.0073,-0.3350,-0.0282,-0.2263,0.4103,0.4910,-0.1015,-0.5462,-0.0561,0.5720,-0.7131,0.5040,0.0258,-0.1281,0.4353,0.0066,-1.0092,-0.3788,0.4802,0.7396,-0.1501,-0.1204,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,-10.0000,0.0000,0.1635,-0.0874,0.4030,0.5088,0.2883,0.6142,0.0193,-0.3163,-0.7598,-0.2473,0.1519,0.1224,-0.8360,0.1114,-0.7122,0.3015,0.0652,-0.2466,0.5076,0.1553,0.0821,0.0378,0.1174,0.1984,0.2513,-0.1817,-0.2907,0.1858,-0.6960,0.3326,0.4012,-0.0227,-0.0009,0.0017,-0.6717,0.0847,0.1819,0.1764,0.0978,-0.0787,-0.1737,-0.0348,0.0184,-0.0544,0.7254,-0.0577,-0.0591,0.1692,-0.6955,0.2421,0.0782,-0.1674,-0.0323,-0.1852,-0.5414,-0.1062,-0.1320,0.1120,0.5533,0.5479}
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Dinucleotide(d=6): {-0.1639,0.0694,-0.0103,0.1344,0.1862,0.0316,0.0327,0.0516,-0.1982,-0.0328,0.0484,-0.0276,-0.2247,0.1123,0.0689,-0.1637,-0.0399,0.0771,-0.0622,0.1777,-0.0233,0.1832,0.2021,-0.1953,0.1135,-0.0527,0.0330,0.1890,-0.1248,-0.1533,0.0398,-0.1028,-0.0668,0.0184,0.0382,-0.0024,0.1217,-0.1414,0.1852,0.0128,0.0773,0.0268,-0.0585,-0.1360,-0.0252,-0.1620,-0.0190,0.0987,0.0050,0.2416,0.0611,0.0257,0.1814,-0.3237,0.1149,0.1370,-0.0216,0.1791,0.0083,0.1683,0.0854,-0.0059,-0.0897,-0.0603,0.1128,0.0591,0.0811,0.0192,-0.2394,0.0551,0.0710,-0.0472,-0.1827,-0.0888,0.2313,0.1779,-0.0083,0.2349,0.2612,0.0950,-0.1146,-0.1229,0.3418,-0.0183,-0.1986,-0.0226,0.1082,0.1248,0.0306,-0.1553,0.0945,0.1114,0.1678,0.1474,-0.0661,0.1877,-0.1297,-0.3666,-0.2263,-0.0462,0.0539,-0.0344,-0.0049,0.0245,0.0791,0.0496,-0.1267,-0.0055,-0.0318,0.0877,-0.0182,-0.2983,0.0114,0.2483,-0.0818,-0.0760,-0.0883,0.0433,0.0670,0.0890,0.0776,-0.0014,-0.0945,0.1197,0.0397,0.1414,0.0203,0.0227,0.0640,-0.2226,-0.1005,-0.0029,0.2321,-0.1604,0.0983,0.0292,-0.0206,-0.0680,-0.0735,0.1213,0.0358,-0.2111,0.0071,0.1758,-0.0116,0.0598,-0.0077,-0.0442,0.1581,-0.0401,0.0973,0.0129,0.0343,-0.0639,-0.1861,0.1229,-0.0776,-0.1215,-0.0987,-0.0400,-0.0187,0.2983,-0.2129,-0.1335,0.1651,-0.0220,-0.0724,-0.1179,0.1689,0.1178,-0.0010,-0.0763,0.0335,-0.0486,-0.1754,-0.0808,-0.1949,0.1559,-0.0766,-0.0011,-0.0129,-0.1953,0.0343,0.1977,-0.2240,0.0432,0.1113,-0.1053,0.0165,-0.1716,-0.0007,-0.1399,0.0956,0.0643,-0.0709,-0.0135,0.0846,-0.1034,0.1322,0.0970,0.0010,-0.1018,0.0641,0.2111,0.0535,0.0494,-0.2107,0.1436,-0.0068,-0.1216,0.0440,-0.0137,-0.0914,0.0083,0.0510,-0.0035,0.0964,-0.1128,0.0948,-0.1260,0.0813,-0.0301,0.0240,-0.1553,0.1883,-0.2527,-0.0152,-0.0277,0.1259,0.0950,-0.0897,0.0755,-0.2363,0.1584,0.0771,0.1520,0.1118,-0.1870,0.0633,0.0934,-0.0035,0.0662,-0.0133,-0.3962,0.2047,-0.0375,-0.0557,0.0126,0.0912,0.0112,-0.2618,0.0899,0.0152,-0.1601,-0.1245,-0.0725,0.1519,0.1464,0.2754,-0.1437,-0.0131,0.0978,-0.1787,-0.1301,-0.1108,-0.0736,-0.0038,-0.1606,-0.0956,0.2654,-0.1412,-0.0030,0.0906,-0.0562,0.2608,-0.3154,0.2339,0.2491,0.1147,0.0113,0.0280,-0.0544,-0.1055,0.0970,0.1355,-0.1089,-0.1243,-0.0200,-0.0692,0.1146,0.1056,-0.0022,-0.0059,-0.1544,-0.5125,-0.0278,-0.2581,0.2161,0.0173,0.2500,-0.0576,0.0795,-0.1264,-0.0240,0.2776,0.1340,-0.1425,0.1692,-0.2413,0.1493,0.0368,-0.0946,-0.1294,-0.2269,-0.0274,-0.0438,0.0910,0.1192,0.0956,0.0306,-0.0537,-0.1305,-0.1765,-0.0985,0.3306,-0.0437,0.0343,0.2662,-0.0248,0.0785,0.1976,0.0743,-0.1963,-0.0432,-0.1054,-0.1521,-0.1951,-0.0504,0.1170,0.0737,-0.0949,0.1268,0.2038,-0.1105,-0.2269,0.0269,0.1230,-0.2602,-0.0105,0.0520,0.0211,-0.0031,0.1122,0.1972,-0.1216,-0.0407,-0.1805,-0.0161,-0.1727,0.0844,-0.0598,-0.1497,0.0927,0.3519,-0.3014,0.3064,0.1429,-0.2456,-0.1639,-0.2298,-0.0769,0.2595,0.0627,0.1088,0.0473,0.0842,0.0970,-0.2227,-0.0954,-0.3276,0.0828,0.0091,0.0416,-0.0770,0.0063,-0.2226,0.0581,-0.0058,0.0288,0.0283,-0.0387,0.0094,0.0029,0.0066,-0.0595,-0.0315,0.0499,-0.0749,-0.0094,0.0092}
Activity(exp=0): {-0.0029,-0.0361}
Activity(exp=1): {-0.0029,-0.0361}
Activity(exp=2): {-0.0029,-0.0361}
> Optimization done.
Probound Model
±
Optimized model:
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Viewer
±
Binding Mode 0
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Binding Mode 1
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Mononucleotide (7bp)
Dinucleotide (7bp)
