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": 200, "nThreads": 20, "lambdaL2": 1e-06}, {"function": "lbfgsSettings", "maxIters": 1000}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.0.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.1.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.2.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.3.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.4.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.5.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.6.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.7.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addTable", "leftFlank": "GGGGAGTTCTACAGTCCGACGATC", "nColumns": 2, "modeledColumns": [0, 1], "countTableFile": "jobs/c9b263b23beb/countTable.8.tsv.gz", "rightFlank": "TGGAATTCTCGGGTGTCAAGG", "inputFileType": "tsv.gz", "variableRegionLength": 40}, {"function": "addSELEX", "concentration": 1, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 4, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 14, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 40, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 121, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 365, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 1100, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 3300, "bindingSaturation": true}, {"function": "addSELEX", "concentration": 9800, "bindingSaturation": true}, {"function": "addNS"}, {"function": "addBindingMode", "flankLength": 6, "singleStrand": true, "dinucleotideDistance": 10, "size": 10}, {"function": "bindingModeConstraints", "index": 1, "roundSpecificActivity": false, "experimentSpecificActivity": false}, {"function": "bindingModeSeed", "index": 1, "mononucleotideString": "..TGCATG.."}, {"function": "output", "outputPath": "jobs/c9b263b23beb", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]Configuration File
±
ProBound configuration file:
{
"modelSeeding": {"bindingModes": [
{"seedScale": 1},
{
"seedScale": 1,
"mononucleotideString": "..TGCATG.."
}
]},
"optimizerSetting": {
"nThreads": 20,
"likelihoodThreshold": 0,
"lambdaL2": 1.0E-6,
"pseudocount": 200,
"patternSearchSettings": {},
"minimizerType": "lbfgs",
"nRetries": 3,
"hkSettings": {},
"output": {
"storeHessian": false,
"outputPath": "jobs/c9b263b23beb",
"printTrajectory": false,
"baseName": "fit",
"printPSAM": false,
"verbose": true
},
"lbfgsSettings": {
"memory": 100,
"convergence": 1.0E-7,
"MCSearch": true,
"maxIters": 1000
},
"sgdSettings": {},
"fixedLibrarySize": false,
"expBound": 40,
"slbfgs_plsSettings": {},
"slbfgsSettings": {}
},
"modelSettings": {
"enrichmentModel": [
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 4,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 14,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 40,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 121,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 365,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 1100,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 3300,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": true,
"concentration": 9800,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
}
],
"countTable": [
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.0.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.1.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.2.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.3.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.4.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.5.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.6.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.7.tsv.gz"
},
{
"leftFlank": "GGGGAGTTCTACAGTCCGACGATC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 40,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "TGGAATTCTCGGGTGTCAAGG",
"countTableFile": "jobs/c9b263b23beb/countTable.8.tsv.gz"
}
],
"bindingModeInteractions": [],
"bindingModes": [
{
"size": 0,
"fitLogActivity": true,
"flankLength": 0,
"dinucleotideDistance": 0,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 10,
"fitLogActivity": true,
"flankLength": 6,
"dinucleotideDistance": 10,
"positionBias": false,
"singleStrand": true,
"modifications": []
}
],
"letterComplement": "C-G,A-T"
},
"modelFittingConstraints": {
"enrichmentModel": [
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [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,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": false,
"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],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[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,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":false,"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,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":false,"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],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}]
> Builds likelihood object.
>> Creating CombinedLikelihood object.
Alphabet
========
Letter Complement: C-G,A-T
Letter Order: ACGT
Optimizer settings:
===================
lambdaL2 = 1.0E-6
pseudocount = 200.0
expBound = 40.0
fixedLibrarySize = false
>> Determining fitting order.
Summary of experiments
======================
Experiment 0:
-------------
Count table: Count table 0
Enrichment model: SELEX enrichment model 0
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 1:
-------------
Count table: Count table 1
Enrichment model: SELEX enrichment model 1
Concentration: 4.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 2:
-------------
Count table: Count table 2
Enrichment model: SELEX enrichment model 2
Concentration: 14.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 3:
-------------
Count table: Count table 3
Enrichment model: SELEX enrichment model 3
Concentration: 40.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 4:
-------------
Count table: Count table 4
Enrichment model: SELEX enrichment model 4
Concentration: 121.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 5:
-------------
Count table: Count table 5
Enrichment model: SELEX enrichment model 5
Concentration: 365.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 6:
-------------
Count table: Count table 6
Enrichment model: SELEX enrichment model 6
Concentration: 1100.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 7:
-------------
Count table: Count table 7
Enrichment model: SELEX enrichment model 7
Concentration: 3300.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 8:
-------------
Count table: Count table 8
Enrichment model: SELEX enrichment model 8
Concentration: 9800.0
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 23:48:15.478).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]},{"h":[8,9]},{"h":[10,11]},{"h":[12,13]},{"h":[14,15]},{"h":[16,17]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 33.322085397046074
gradient = {0.4994,-0.4994,0.4994,-0.4994,0.4994,-0.4994,0.4994,-0.4994,0.4994,-0.4994,0.4994,-0.4994,0.4994,-0.4994,0.4994,-0.4994,0.4994,-0.4994}
gradient norm = 2.118736518536731
Starting Function Value: 33.322085397046074
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 22.767753326141122 5.000000000000001 2.359897021765200 2.094184456577549
2 7 6.252724967937597 10.491309427519266 0.024599865430992 0.106357021582803
3 9 6.241398948060764 0.212777727774126 0.379060895267689 0.000057062751072
4 10 6.241398944802993 0.212777727774126 1.000000000000000 0.000000047953412
Convergence criteria met.
After: gradient norm = 4.7953412367837224E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {-3.7015,3.7015}
Count Table 1:
---------------
h: {-3.7015,3.7015}
Count Table 2:
---------------
h: {-3.7015,3.7015}
Count Table 3:
---------------
h: {-3.7015,3.7015}
Count Table 4:
---------------
h: {-3.7015,3.7015}
Count Table 5:
---------------
h: {-3.7015,3.7015}
Count Table 6:
---------------
h: {-3.7015,3.7015}
Count Table 7:
---------------
h: {-3.7015,3.7015}
Count Table 8:
---------------
h: {-3.7015,3.7015}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-7.4025,-7.4025}
Activity(exp=1): {-8.7887,-8.7887}
Activity(exp=2): {-10.0415,-10.0415}
Activity(exp=3): {-11.0913,-11.0913}
Activity(exp=4): {-12.1982,-12.1982}
Activity(exp=5): {-13.3023,-13.3023}
Activity(exp=6): {-14.4055,-14.4055}
Activity(exp=7): {-15.5041,-15.5041}
Activity(exp=8): {-16.5926,-16.5926}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=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}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Activity(exp=6): {0.0000,0.0000}
Activity(exp=7): {0.0000,0.0000}
Activity(exp=8): {0.0000,0.0000}
> Initial optimization (component0-1-f0).
>> Starting new optimization: component0-1-f0. (2021-05-21 23:48:18.008).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[18,19]},{"h":[20,21]},{"h":[22,23]},{"h":[24,25]},{"h":[26,27]},{"h":[28,29]},{"h":[30,31]},{"h":[32,33]},{"h":[34,35]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11],[12,13],[14,15],[16,17]]},{}]}
Value and gradient before optimization:
=======================================
value = 6.241398945008458
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}
gradient norm = 1.223128464978287E-4
Starting Function Value: 6.241398945008458
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 6.241398896965674 0.000783021571522 6.401793384280118 0.000238122291748
2 9 6.241296822602681 0.957672641592181 1365.0000000000000 0.001401849807755
3 11 6.240283187976049 10.518223215597539 0.263162743320643 0.001811309260762
4 14 6.240125402517785 2.135744233059489 0.029476580126717 0.005921254720686
5 17 6.240016848581495 1.588713368554535 0.046908147017510 0.007929796718113
6 19 6.239929239915211 1.814437371050959 0.321745132433739 0.011782601555354
7 20 6.239834890833852 1.846591502414190 1.000000000000000 0.014013133073469
8 21 6.239670244787073 0.762425199341358 1.000000000000000 0.005876003187067
9 22 6.239585043592382 2.013162889751169 1.000000000000000 0.010293467667690
10 23 6.239487079716466 0.736893127511307 1.000000000000000 0.006089031417028
11 25 6.239433374066979 0.930471590629544 0.464675290128204 0.006673432724860
12 26 6.239398858066301 1.058418099769552 1.000000000000000 0.009234721015792
13 27 6.239375090607334 0.458814762249544 1.000000000000000 0.003880853157444
14 28 6.239360870351306 0.712907291378232 1.000000000000000 0.007502190224009
15 29 6.239319411993824 0.147683722397082 1.000000000000000 0.003122084040608
16 30 6.239293495114849 0.550178652865884 1.000000000000000 0.004299417805437
17 31 6.239246317753503 0.779071671188732 1.000000000000000 0.004091342760786
18 32 6.239222953844100 0.932603927999945 1.000000000000000 0.007239790094163
19 33 6.239141485016831 0.832503053699145 1.000000000000000 0.003097287696971
20 35 6.239131131720474 0.270702569883961 0.183257780443969 0.003914959824804
21 36 6.239112187305778 0.512222815276588 1.000000000000000 0.004913910419691
22 37 6.239093672392632 0.074086868999450 1.000000000000000 0.002568184349364
23 38 6.239074578283850 0.451688159729487 1.000000000000000 0.003437359652313
24 40 6.239056723978468 0.497650334363644 0.515805934655253 0.004573926451260
25 41 6.239021924654290 0.538937672856811 1.000000000000000 0.003635925807554
26 42 6.238999794427683 0.293731444874219 1.000000000000000 0.001944764578882
27 44 6.238991513904320 0.269858403800022 0.185067590898733 0.003137078180539
28 45 6.238978159353797 0.762876268060336 1.000000000000000 0.006002592859006
29 46 6.238954575400860 0.118529003333678 1.000000000000000 0.001780774724729
30 47 6.238937767578646 0.331056593517347 1.000000000000000 0.001337369319407
31 49 6.238927459720980 0.327781621612341 0.178643364071168 0.002737305572173
32 50 6.238917028478629 0.399066372134693 1.000000000000000 0.004102735612170
33 51 6.238902896328886 0.108677085393622 1.000000000000000 0.002614401887309
34 52 6.238879593337711 0.606868800687079 1.000000000000000 0.003411070339743
35 53 6.238858790401998 0.458989695990332 1.000000000000000 0.003312299488756
36 54 6.238838910361591 0.318308572126693 1.000000000000000 0.002170542256020
37 56 6.238831819318233 0.248115459393408 0.171806524258402 0.002989225665351
38 58 6.238820315026557 0.304175376696182 0.404423042025520 0.003169742966792
39 59 6.238801545096603 0.463911065165668 1.000000000000000 0.003288680846448
40 60 6.238791470654929 0.100624546341532 1.000000000000000 0.002173507535952
41 61 6.238777106663143 0.802933873429865 1.000000000000000 0.004966436265723
42 62 6.238763058453505 0.176914065892016 1.000000000000000 0.001023569082682
43 63 6.238748986694262 0.375313465289238 1.000000000000000 0.001413660029382
44 65 6.238740230231044 0.339363261347621 0.256252121883796 0.002629393879673
45 66 6.238729671930836 0.466917939740978 1.000000000000000 0.003897238173912
46 67 6.238712037063883 0.228308344480416 1.000000000000000 0.002287279766152
47 68 6.238700233000604 0.780408119872464 1.000000000000000 0.004834298185670
48 69 6.238675802002571 0.459090275686399 1.000000000000000 0.004011211547891
49 70 6.238664187792589 0.628332885243427 1.000000000000000 0.005082291178576
50 71 6.238656991595814 0.238974838400651 1.000000000000000 0.003156703386235
51 72 6.238641635542464 0.240646644462280 1.000000000000000 0.001008036481395
52 73 6.238635496836760 0.488002469457547 1.000000000000000 0.003469749361909
53 74 6.238626528075064 0.039032887729162 1.000000000000000 0.001954524013833
54 75 6.238609618591104 0.504914549543465 1.000000000000000 0.001795855004706
55 77 6.238599873939272 0.440112762196792 0.420909499757525 0.002729634689615
56 78 6.238584492088462 0.540049008901055 1.000000000000000 0.002930727873773
57 80 6.238575776716379 0.163815981296133 0.439567353620319 0.002195900885094
58 82 6.238562826837794 0.435677689176368 0.445156304962387 0.002104441254364
59 84 6.238555480229593 0.358626693497452 0.200297117685915 0.002719106752887
60 85 6.238545603412517 0.375300089011564 1.000000000000000 0.002817492444397
61 86 6.238538238408747 0.118272095552070 1.000000000000000 0.001863668235999
62 87 6.238529618181461 0.928360487447640 1.000000000000000 0.004487891409672
63 88 6.238513879677162 0.105196377593958 1.000000000000000 0.000589527952217
64 89 6.238501260346748 0.544356374467170 1.000000000000000 0.001161322787312
65 91 6.238495748946857 0.376207614804731 0.266034233232493 0.002264537543542
66 92 6.238487121741370 0.497987986050386 1.000000000000000 0.002876502181122
67 93 6.238472012761092 0.481545227295576 1.000000000000000 0.001851009553704
68 94 6.238461158433867 0.852078656868553 1.000000000000000 0.003283393298425
69 95 6.238460542694202 0.153975670986998 1.000000000000000 0.003572619641861
70 96 6.238438607210385 0.619847680333302 1.000000000000000 0.001573874595415
71 97 6.238434667723960 0.451043269752137 1.000000000000000 0.002633764836275
72 98 6.238428934922291 0.159511441255550 1.000000000000000 0.001879264064906
73 99 6.238420014128954 0.479466188933121 1.000000000000000 0.001643365068159
74 100 6.238414382117706 0.930762275569106 1.000000000000000 0.003460102552049
75 101 6.238413129232290 0.231164507873230 1.000000000000000 0.002575478962088
76 102 6.238403733849083 0.219032669538305 1.000000000000000 0.000641804444437
77 103 6.238399931537305 0.528176884391696 1.000000000000000 0.002044833438163
78 104 6.238395729769489 0.172148291105518 1.000000000000000 0.001447832161954
79 105 6.238387577785565 0.839358341666486 1.000000000000000 0.002069212955079
80 106 6.238378593392258 0.507963177382516 1.000000000000000 0.000729837447965
81 108 6.238373832493707 0.507123275019391 0.318501511765271 0.000878971520209
82 110 6.238372110398988 0.344445419805602 0.364709437395958 0.001492562178941
83 111 6.238369437715964 0.279844320756240 1.000000000000000 0.001352590124285
84 112 6.238365121138338 0.433736981628774 1.000000000000000 0.000848940174169
85 114 6.238363287517048 0.353766710705184 0.406655977563842 0.001152445913754
86 115 6.238358740862556 0.865640551969798 1.000000000000000 0.001289876668495
87 116 6.238356897665621 0.188030552215959 1.000000000000000 0.000778104583827
88 117 6.238354585743022 0.649013180646421 1.000000000000000 0.000841135027781
89 118 6.238353891541808 0.079256112731803 1.000000000000000 0.000474788360339
90 119 6.238353371356372 0.725354835215444 1.000000000000000 0.001145839626864
91 120 6.238352399010105 0.124880891076878 1.000000000000000 0.000318618743048
92 121 6.238352020285682 0.203208054306999 1.000000000000000 0.000148225512874
93 123 6.238351825648805 0.207020855803871 0.426855027993751 0.000228252713178
94 124 6.238351703436653 0.191508832216663 1.000000000000000 0.000247478504409
95 125 6.238351619216912 0.091854533818137 1.000000000000000 0.000109984159426
96 126 6.238351587351960 0.112496022850320 1.000000000000000 0.000047449426124
97 127 6.238351583174098 0.029894935607662 1.000000000000000 0.000009425624273
98 128 6.238351582886091 0.016203896461047 1.000000000000000 0.000006640531501
99 129 6.238351582530517 0.000403640981632 1.000000000000000 0.000007400682950
100 130 6.238351576533834 0.007295599408367 1.000000000000000 0.000049595824731
101 131 6.238351567324106 0.008337104863421 1.000000000000000 0.000091477995711
102 132 6.238351536934006 0.021900843215191 1.000000000000000 0.000177653801945
103 133 6.238351464254708 0.045539399414056 1.000000000000000 0.000301709993444
104 134 6.238351269881791 0.117657113557309 1.000000000000000 0.000491877004206
105 135 6.238350766199099 0.330658332339132 1.000000000000000 0.000706130441186
106 136 6.238350113694321 0.877961371852414 1.000000000000000 0.000911802557358
107 137 6.238349033984309 0.545142082046977 1.000000000000000 0.001488110197375
108 138 6.238347871432743 0.212321999612744 1.000000000000000 0.001062593269419
109 139 6.238346793288040 1.035191572105981 1.000000000000000 0.000535389629368
110 141 6.238345839320769 0.273184453367103 0.488135947361975 0.000516154944915
111 142 6.238345289653036 0.182242187728945 1.000000000000000 0.000475209710201
112 143 6.238344307034156 0.523627188009423 1.000000000000000 0.000558068995717
113 144 6.238343634012196 0.721042622100641 1.000000000000000 0.000790676012434
114 145 6.238343590232034 0.357676604514590 1.000000000000000 0.000634902028721
115 146 6.238343156817233 0.175252030089745 1.000000000000000 0.000040623890050
116 147 6.238343080340692 0.199444042652280 1.000000000000000 0.000276342053618
117 148 6.238343037091314 0.019666692998110 1.000000000000000 0.000178150346942
118 149 6.238342974020594 0.101021909895396 1.000000000000000 0.000086358990237
119 150 6.238342943606518 0.095593840138229 1.000000000000000 0.000052784870408
120 151 6.238342931763537 0.077833627080779 1.000000000000000 0.000029101300867
121 152 6.238342929785518 0.023625255509969 1.000000000000000 0.000023134846581
122 153 6.238342928805765 0.017076920697683 1.000000000000000 0.000009581275314
123 154 6.238342928599332 0.010303203787539 1.000000000000000 0.000002598569793
124 155 6.238342928591510 0.000807268366483 1.000000000000000 0.000000727923795
125 156 6.238342928590984 0.000637438153385 1.000000000000000 0.000000632542040
126 157 6.238342928588642 0.000333772734445 1.000000000000000 0.000000654089409
127 158 6.238342928577803 0.001352839313337 1.000000000000000 0.000001606262622
128 159 6.238342928556508 0.001494355421876 1.000000000000000 0.000003037827835
129 160 6.238342928493482 0.002769161814092 1.000000000000000 0.000005833029827
130 161 6.238342928337071 0.004241656528169 1.000000000000000 0.000010168377925
131 162 6.238342927920614 0.007051478932182 1.000000000000000 0.000017337244122
132 163 6.238342926851288 0.011622573723864 1.000000000000000 0.000028581479490
133 164 6.238342924216443 0.019648959908505 1.000000000000000 0.000045605709557
134 165 6.238342918838974 0.031544093527774 1.000000000000000 0.000067814566330
135 166 6.238342911202462 0.037755692887086 1.000000000000000 0.000084989456849
136 167 6.238342903472796 0.039796460990837 1.000000000000000 0.000094746968551
137 168 6.238342889921580 0.030573596013809 1.000000000000000 0.000060685460037
138 169 6.238342879635564 0.041848827285985 1.000000000000000 0.000026829418166
139 171 6.238342874664714 0.034298564152870 0.326977568198497 0.000030689966958
140 172 6.238342872543621 0.031523106113906 1.000000000000000 0.000050094649128
141 173 6.238342870246937 0.009333065008918 1.000000000000000 0.000017915168275
142 174 6.238342868993084 0.017829557278342 1.000000000000000 0.000012236824479
143 175 6.238342868334049 0.019851916667222 1.000000000000000 0.000013715320533
144 176 6.238342868199031 0.011219394310819 1.000000000000000 0.000011539281230
145 177 6.238342868093100 0.005109504536940 1.000000000000000 0.000004385736684
146 178 6.238342868068148 0.002374252373228 1.000000000000000 0.000002113878167
147 179 6.238342868063647 0.000616281812959 1.000000000000000 0.000000436496816
148 180 6.238342868063532 0.000205221069925 1.000000000000000 0.000000101843720
149 181 6.238342868063187 0.000205221069925 1.000000000000000 0.000000056909762
Convergence criteria met.
After: gradient norm = 5.6909761753108373E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.3153,0.3153}
Count Table 1:
---------------
h: {-0.1082,0.1082}
Count Table 2:
---------------
h: {-0.0344,0.0344}
Count Table 3:
---------------
h: {-0.0124,0.0124}
Count Table 4:
---------------
h: {-0.0041,0.0041}
Count Table 5:
---------------
h: {-0.0014,0.0014}
Count Table 6:
---------------
h: {-0.0005,0.0005}
Count Table 7:
---------------
h: {-0.0002,0.0002}
Count Table 8:
---------------
h: {-0.0001,0.0001}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.1294}
Activity(exp=1): {0.0004,0.0339}
Activity(exp=2): {0.0004,0.0025}
Activity(exp=3): {0.0004,-0.0039}
Activity(exp=4): {0.0005,0.0100}
Activity(exp=5): {0.0005,0.0028}
Activity(exp=6): {0.0006,-0.0028}
Activity(exp=7): {0.0006,-0.0079}
Activity(exp=8): {0.0007,0.0014}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=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}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Activity(exp=6): {0.0000,0.0000}
Activity(exp=7): {0.0000,0.0000}
Activity(exp=8): {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 23:48:36.573).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[18,19]},{"h":[20,21]},{"h":[22,23]},{"h":[24,25]},{"h":[26,27]},{"h":[28,29]},{"h":[30,31]},{"h":[32,33]},{"h":[34,35]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11],[12,13],[14,15],[16,17]]},{}]}
Value and gradient before optimization:
=======================================
value = 6.238342868063189
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}
gradient norm = 5.6909761753346515E-8
Already at minimum!
After: gradient norm = 5.6909761753346515E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.3153,0.3153}
Count Table 1:
---------------
h: {-0.1082,0.1082}
Count Table 2:
---------------
h: {-0.0344,0.0344}
Count Table 3:
---------------
h: {-0.0124,0.0124}
Count Table 4:
---------------
h: {-0.0041,0.0041}
Count Table 5:
---------------
h: {-0.0014,0.0014}
Count Table 6:
---------------
h: {-0.0005,0.0005}
Count Table 7:
---------------
h: {-0.0002,0.0002}
Count Table 8:
---------------
h: {-0.0001,0.0001}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.1294}
Activity(exp=1): {0.0004,0.0339}
Activity(exp=2): {0.0004,0.0025}
Activity(exp=3): {0.0004,-0.0039}
Activity(exp=4): {0.0005,0.0100}
Activity(exp=5): {0.0005,0.0028}
Activity(exp=6): {0.0006,-0.0028}
Activity(exp=7): {0.0006,-0.0079}
Activity(exp=8): {0.0007,0.0014}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=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}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Activity(exp=6): {0.0000,0.0000}
Activity(exp=7): {0.0000,0.0000}
Activity(exp=8): {0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component0-2-variation0.
> No varitions possible for Binding mode 0.
> Optimizing the full model (component0-4-all).
>> Starting new optimization: component0-4-all. (2021-05-21 23:48:36.684).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[18,19]},{"h":[20,21]},{"h":[22,23]},{"h":[24,25]},{"h":[26,27]},{"h":[28,29]},{"h":[30,31]},{"h":[32,33]},{"h":[34,35]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11],[12,13],[14,15],[16,17]]},{}]}
Value and gradient before optimization:
=======================================
value = 6.238342868063189
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}
gradient norm = 5.690976175329475E-8
Already at minimum!
After: gradient norm = 5.690976175329475E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.3153,0.3153}
Count Table 1:
---------------
h: {-0.1082,0.1082}
Count Table 2:
---------------
h: {-0.0344,0.0344}
Count Table 3:
---------------
h: {-0.0124,0.0124}
Count Table 4:
---------------
h: {-0.0041,0.0041}
Count Table 5:
---------------
h: {-0.0014,0.0014}
Count Table 6:
---------------
h: {-0.0005,0.0005}
Count Table 7:
---------------
h: {-0.0002,0.0002}
Count Table 8:
---------------
h: {-0.0001,0.0001}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0003,0.1294}
Activity(exp=1): {0.0004,0.0339}
Activity(exp=2): {0.0004,0.0025}
Activity(exp=3): {0.0004,-0.0039}
Activity(exp=4): {0.0005,0.0100}
Activity(exp=5): {0.0005,0.0028}
Activity(exp=6): {0.0006,-0.0028}
Activity(exp=7): {0.0006,-0.0079}
Activity(exp=8): {0.0007,0.0014}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=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}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Activity(exp=6): {0.0000,0.0000}
Activity(exp=7): {0.0000,0.0000}
Activity(exp=8): {0.0000,0.0000}
==================================
== Starts fiting Binding mode 1 ==
==================================
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 0 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {86.1254,97.9988}
Shift in SELEXModel.activationAdjustment = Log[4.3476276568669655E-4/86.12544932818476] = -12.196514988362788
Shift in SELEXModel.activationAdjustment = Log[4.3476276568669655E-4/97.99884777937915] = -12.325665763127505
Expected partition function after adjustment: {0.0004,0.0004}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 1 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {344.5209,356.2595}
Shift in SELEXModel.activationAdjustment = Log[0.0017390510627467862/344.52086479297014] = -12.196570334815915
Shift in SELEXModel.activationAdjustment = Log[0.0017390510627467862/356.2594503699741] = -12.230074939344766
Expected partition function after adjustment: {0.0017,0.0017}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 2 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {1205.8833,1208.4755}
Shift in SELEXModel.activationAdjustment = Log[0.006086678719613751/1205.883338347418] = -12.196620350500169
Shift in SELEXModel.activationAdjustment = Log[0.006086678719613751/1208.4754520252516] = -12.19876759943775
Expected partition function after adjustment: {0.0061,0.0061}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 3 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {3445.5254,3430.4554}
Shift in SELEXModel.activationAdjustment = Log[0.01739051062746786/3445.5253802122884] = -12.19666226472687
Shift in SELEXModel.activationAdjustment = Log[0.01739051062746786/3430.4554372520415] = -12.192278899650773
Expected partition function after adjustment: {0.0174,0.0174}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 4 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {10423.1749,10522.7986}
Shift in SELEXModel.activationAdjustment = Log[0.05260629464809028/10423.174927448868] = -12.196706460712207
Shift in SELEXModel.activationAdjustment = Log[0.05260629464809028/10522.798610987416] = -12.206218974855602
Expected partition function after adjustment: {0.0526,0.0526}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 5 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {31443.1950,31515.4894}
Shift in SELEXModel.activationAdjustment = Log[0.15868840947564422/31443.19501409731] = -12.196750552262545
Shift in SELEXModel.activationAdjustment = Log[0.15868840947564422/31515.489373365177] = -12.199047118391457
Expected partition function after adjustment: {0.1587,0.1587}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 6 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {94764.4906,94441.6483}
Shift in SELEXModel.activationAdjustment = Log[0.4782390422553662/94764.49055831647] = -12.196794628996642
Shift in SELEXModel.activationAdjustment = Log[0.4782390422553662/94441.64828132244] = -12.19338202735181
Expected partition function after adjustment: {0.4782,0.4782}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 7 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {284305.9702,281885.1600}
Shift in SELEXModel.activationAdjustment = Log[1.4347171267660985/284305.9701890526] = -12.19683859145311
Shift in SELEXModel.activationAdjustment = Log[1.4347171267660985/281885.16004536464] = -12.188287327521083
Expected partition function after adjustment: {1.4347,1.4347}
>>> Binding mode 1 is the first sequence-specific componenent in SELEX enrichment model 8 and this enrichment model has bindingSaturation=true.
Expected partition function before adjustment: {844339.5219,844981.3188}
Shift in SELEXModel.activationAdjustment = Log[4.260675103729626/844339.5218782218] = -12.196882347013913
Shift in SELEXModel.activationAdjustment = Log[4.260675103729626/844981.3188121347] = -12.197642175400956
Expected partition function after adjustment: {4.2607,4.2607}
> Optimizing h (component1-0-h).
>> Starting new optimization: component1-0-h. (2021-05-21 23:48:37.816).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]},{"h":[8,9]},{"h":[10,11]},{"h":[12,13]},{"h":[14,15]},{"h":[16,17]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 28.33028749609639
gradient = {0.5000,-0.4999,0.5000,-0.4999,0.4998,-0.4998,0.4994,-0.4994,0.4981,-0.4981,0.4941,-0.4941,0.4833,-0.4833,0.4540,-0.4539,0.3852,-0.3851}
gradient norm = 2.039262115559173
Starting Function Value: 28.33028749609639
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 26.226327772982910 1.000000000000000 0.490373450460436 2.005832465136485
2 5 9.069034915015810 11.649509645215794 0.108944902292533 1.293377347063524
3 7 7.090085818833027 2.854522020577322 0.280682692611689 0.895745313536889
4 8 6.524255433724626 3.119483426799936 1.000000000000000 0.590749105012969
5 9 6.150140861920169 1.356433239001681 1.000000000000000 0.095173551178550
6 10 6.143934254450589 0.291927702202819 1.000000000000000 0.053942477708056
7 11 6.141006868892239 0.110432224888749 1.000000000000000 0.002406359643025
8 12 6.141001106565733 0.005387560443181 1.000000000000000 0.000304298343083
9 13 6.141001004655546 0.000599672813595 1.000000000000000 0.000103656492728
10 14 6.141000978691277 0.000272741045085 1.000000000000000 0.000109114621957
11 15 6.141000638031249 0.004569071025933 1.000000000000000 0.000372521404122
12 16 6.141000008965846 0.009880876989862 1.000000000000000 0.000726331922287
13 17 6.140998096701422 0.032615940952808 1.000000000000000 0.001406701172795
14 18 6.140993362567158 0.084857118578382 1.000000000000000 0.002447287587309
15 19 6.140980754946165 0.232827821451532 1.000000000000000 0.004159718027022
16 20 6.140948360233724 0.609913923794270 1.000000000000000 0.006860228371338
17 21 6.140865625919260 1.580880479933563 1.000000000000000 0.011044572374123
18 22 6.140664293413935 3.910952490302036 1.000000000000000 0.017008792583551
19 23 6.140224443893666 8.781845409045106 1.000000000000000 0.023798531962560
20 24 6.139478852363682 15.663760429225873 1.000000000000000 0.026811986276744
21 25 6.138717130165919 17.090093427647517 1.000000000000000 0.019512353937771
22 26 6.138374814323497 6.706458818296889 1.000000000000000 0.006807161466741
23 27 6.138322072312798 1.540106984167424 1.000000000000000 0.000727965897580
24 28 6.138319647524197 1.216392522590385 1.000000000000000 0.000043316012121
25 29 6.138319617851089 0.166567612942380 1.000000000000000 0.000033458885176
26 31 6.138319616763161 0.006367485185001 0.093459000203095 0.000006423001736
27 32 6.138319616713496 0.006367485185001 1.000000000000000 0.000000305826994
Convergence criteria met.
After: gradient norm = 3.0582699429556683E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-5.5698,5.5697}
Count Table 1:
---------------
h: {-4.8770,4.8769}
Count Table 2:
---------------
h: {-4.2504,4.2504}
Count Table 3:
---------------
h: {-3.7230,3.7230}
Count Table 4:
---------------
h: {-3.1509,3.1509}
Count Table 5:
---------------
h: {-2.5771,2.5771}
Count Table 6:
---------------
h: {-2.0473,2.0473}
Count Table 7:
---------------
h: {-1.5220,1.5220}
Count Table 8:
---------------
h: {-1.0253,1.0253}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-12.1962,-12.1962}
Activity(exp=1): {-12.1962,-12.1962}
Activity(exp=2): {-12.1962,-12.1962}
Activity(exp=3): {-12.1962,-12.1962}
Activity(exp=4): {-12.1962,-12.1962}
Activity(exp=5): {-12.1962,-12.1962}
Activity(exp=6): {-12.1962,-12.1962}
Activity(exp=7): {-12.1962,-12.1962}
Activity(exp=8): {-12.1962,-12.1962}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=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}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-11.3838,-11.3838}
Activity(exp=1): {-11.3838,-11.3838}
Activity(exp=2): {-11.3838,-11.3838}
Activity(exp=3): {-11.3838,-11.3838}
Activity(exp=4): {-11.3838,-11.3838}
Activity(exp=5): {-11.3838,-11.3838}
Activity(exp=6): {-11.3838,-11.3838}
Activity(exp=7): {-11.3838,-11.3838}
Activity(exp=8): {-11.3838,-11.3838}
> Initial optimization (component1-1-f1).
>> Starting new optimization: component1-1-f1. (2021-05-21 23:49:51.22).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[41,42]},{"h":[43,44]},{"h":[45,46]},{"h":[47,48]},{"h":[49,50]},{"h":[51,52]},{"h":[53,54]},{"h":[55,56]},{"h":[57,58]}],"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],"activity":[[40,40],[40,40],[40,40],[40,40],[40,40],[40,40],[40,40],[40,40],[40,40]]}]}
Value and gradient before optimization:
=======================================
value = 6.196348367626878
gradient = {-0.0160,0.0098,0.0018,-0.0153,-0.0153,0.0115,0.0009,-0.0169,-0.0126,0.0073,0.0042,-0.0187,0.0107,0.0291,-0.0638,0.0043,-0.0031,-0.0170,0.0041,-0.0037,-0.0481,0.0219,0.0073,-0.0007,0.0020,0.0124,0.0070,-0.0411,0.0020,0.0160,-0.0359,-0.0018,-0.0079,0.0044,-0.0028,-0.0134,-0.0216,0.0182,-0.0020,-0.0143,-0.0201,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000}
gradient norm = 0.12319047673445915
Starting Function Value: 6.196348367626878
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 6.189714330278824 0.087881948214610 0.713382645673518 0.167402282516520
2 4 6.179737876949192 0.115258605975026 1.000000000000000 0.209871819178716
3 6 6.143163495286893 0.523101037923164 0.451204682580261 0.359343091172440
4 7 6.116078755272041 0.510530413536223 1.000000000000000 0.359575288170245
5 8 6.086596577978753 0.423614158449874 1.000000000000000 0.087075646714449
6 9 6.079848551840844 0.314920813207346 1.000000000000000 0.052212149566979
7 10 6.074427589468847 0.226537966538087 1.000000000000000 0.034215249355546
8 11 6.071037957822073 0.222238171569760 1.000000000000000 0.022438317812606
9 12 6.068447225443293 0.197002659152164 1.000000000000000 0.026334014709838
10 13 6.066710315753729 0.213413822599595 1.000000000000000 0.023847040965819
11 14 6.065810076951088 0.133607804702154 1.000000000000000 0.018246197617233
12 15 6.064415181447068 0.188121646258066 1.000000000000000 0.016776021530304
13 16 6.063422667535253 0.632040521791749 1.000000000000000 0.055233778953088
14 17 6.061043119320212 0.129398991225784 1.000000000000000 0.022076331194031
15 18 6.060516338058965 0.094411577290507 1.000000000000000 0.010992375197520
16 19 6.059621355799758 0.340417399680110 1.000000000000000 0.018120761264952
17 20 6.058396247854197 0.341915073812229 1.000000000000000 0.015041960247528
18 22 6.057840161299328 0.244781712811096 0.378425548162044 0.028059607006790
19 23 6.056996945742846 0.186408496696627 1.000000000000000 0.014500323346409
20 24 6.056742700433139 0.157926919847739 1.000000000000000 0.021672639072765
21 25 6.056613998274906 0.105411529284892 1.000000000000000 0.007086715036971
22 26 6.056462420168710 0.085306104893405 1.000000000000000 0.008050323933333
23 27 6.056325913070881 0.097864309720251 1.000000000000000 0.011682637892446
24 28 6.056200029434689 0.084908955099311 1.000000000000000 0.009491484804943
25 29 6.056040575312046 0.116056198375218 1.000000000000000 0.006046850132068
26 30 6.055933906670636 0.129693305007633 1.000000000000000 0.004769521612997
27 31 6.055875801114455 0.064361715812705 1.000000000000000 0.002833387636724
28 32 6.055854987459669 0.023730586157696 1.000000000000000 0.003159358190732
29 33 6.055807826857355 0.068029081567939 1.000000000000000 0.003559344978457
30 34 6.055803830424914 0.055979790921158 1.000000000000000 0.004988377628786
31 35 6.055776184701737 0.014294091029566 1.000000000000000 0.001404158003926
32 36 6.055769628920277 0.009928957478172 1.000000000000000 0.001041782718156
33 37 6.055759450677924 0.021903916511345 1.000000000000000 0.001083113433810
34 38 6.055748773611414 0.031753854467585 1.000000000000000 0.001238792744418
35 39 6.055741002092296 0.039670709882845 1.000000000000000 0.001114134666813
36 40 6.055736864081016 0.019061679790583 1.000000000000000 0.001201456830066
37 41 6.055733322527553 0.008271946190469 1.000000000000000 0.000911809471665
38 42 6.055729871224649 0.010349606259407 1.000000000000000 0.000680548429631
39 43 6.055725496217576 0.018021338270856 1.000000000000000 0.000750767423629
40 44 6.055717060554733 0.038330407806189 1.000000000000000 0.001398674477139
41 45 6.055704108970450 0.072252467458265 1.000000000000000 0.001718230973937
42 46 6.055700525136524 0.136526181824470 1.000000000000000 0.004972405715262
43 47 6.055674874396511 0.028799046924826 1.000000000000000 0.002656627953781
44 48 6.055653851619258 0.059413841214064 1.000000000000000 0.001460005376204
45 49 6.055631439428516 0.116345554300571 1.000000000000000 0.002080468206003
46 50 6.055596621687164 0.179609634667385 1.000000000000000 0.002628136044109
47 51 6.055485347888848 0.593510391967724 1.000000000000000 0.003062469390496
48 52 6.055317154082209 1.230592925397475 1.000000000000000 0.009921473509134
49 53 6.055052787185696 1.418474874431832 1.000000000000000 0.005421302886232
50 54 6.054770150849664 1.562899499129890 1.000000000000000 0.003719022694748
51 55 6.054594453160881 0.946385243561800 1.000000000000000 0.005025823754356
52 56 6.054467088366942 0.628686653460070 1.000000000000000 0.003788154881411
53 57 6.054348403441147 0.388297979203018 1.000000000000000 0.003475713962984
54 58 6.054170852883550 0.837451695431003 1.000000000000000 0.004204203773371
55 59 6.053924135610531 1.342103243462747 1.000000000000000 0.006384612741278
56 60 6.053596541683825 2.216143399433680 1.000000000000000 0.005388569604146
57 61 6.053321469113556 1.660262083342431 1.000000000000000 0.003900595491780
58 62 6.053207356772911 0.766338772004950 1.000000000000000 0.003576813160382
59 63 6.053191011837864 0.237612610049474 1.000000000000000 0.001080974362452
60 64 6.053187181143894 0.107304650346314 1.000000000000000 0.000636657720592
61 65 6.053183766382908 0.012114625313579 1.000000000000000 0.000456573472222
62 66 6.053180619820442 0.082333155821553 1.000000000000000 0.000407419898920
63 67 6.053178696768566 0.058062602657402 1.000000000000000 0.000431814776010
64 68 6.053176573801476 0.045196065960909 1.000000000000000 0.000347236645714
65 69 6.053175274650371 0.021885516357132 1.000000000000000 0.000377536389573
66 70 6.053174787866263 0.013719673526843 1.000000000000000 0.000162589228456
67 71 6.053174648861336 0.013693139796610 1.000000000000000 0.000052591776368
68 72 6.053174613443237 0.005857785890649 1.000000000000000 0.000038598961945
69 73 6.053174577657355 0.001532549136648 1.000000000000000 0.000035287545573
70 74 6.053174514005290 0.004105255334397 1.000000000000000 0.000033052660403
71 75 6.053174510525242 0.009521644316068 1.000000000000000 0.000112857198539
72 76 6.053174466525999 0.003359416374597 1.000000000000000 0.000025480071403
73 77 6.053174460976705 0.000443045323956 1.000000000000000 0.000015571718664
74 78 6.053174457239474 0.000726389196513 1.000000000000000 0.000013551505438
75 79 6.053174454597142 0.000628031843567 1.000000000000000 0.000010279900266
76 80 6.053174451618496 0.000955017892555 1.000000000000000 0.000006869330057
77 81 6.053174448690913 0.001274527614739 1.000000000000000 0.000013688282691
78 82 6.053174444717207 0.001759364988080 1.000000000000000 0.000024456832023
79 83 6.053174438514198 0.002794428427920 1.000000000000000 0.000035454788174
80 84 6.053174429717281 0.004093675863198 1.000000000000000 0.000039938804629
81 85 6.053174412586071 0.007077215309707 1.000000000000000 0.000047297841503
82 86 6.053174365693117 0.021772034808811 1.000000000000000 0.000030549048704
83 87 6.053174307482900 0.027434253780497 1.000000000000000 0.000032504227031
84 88 6.053174210779647 0.047510158206923 1.000000000000000 0.000080206433155
85 89 6.053174103145912 0.051950053040696 1.000000000000000 0.000103073698910
86 90 6.053173954587162 0.063114724836705 1.000000000000000 0.000078928289801
87 91 6.053173657287096 0.142121876012689 1.000000000000000 0.000078747784584
88 92 6.053173285226893 0.206574417425449 1.000000000000000 0.000257402660776
89 93 6.053172841041483 0.157797021160467 1.000000000000000 0.000325241433412
90 94 6.053171403008721 0.626908910746753 1.000000000000000 0.000565893698798
91 95 6.053170646588225 0.383114439219240 1.000000000000000 0.000508538292679
92 96 6.053170025673747 0.440804680570882 1.000000000000000 0.000327509716784
93 97 6.053169896556528 0.011386544142768 1.000000000000000 0.000053799920290
94 98 6.053169887611419 0.031645077317318 1.000000000000000 0.000012015489610
95 99 6.053169886773445 0.008566026896868 1.000000000000000 0.000003692358898
96 100 6.053169886602143 0.008566026896868 1.000000000000000 0.000001854202838
Convergence criteria met.
After: gradient norm = 1.8542028379756238E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-5.8697,5.8697}
Count Table 1:
---------------
h: {-5.1770,5.1770}
Count Table 2:
---------------
h: {-4.5508,4.5508}
Count Table 3:
---------------
h: {-4.0176,4.0176}
Count Table 4:
---------------
h: {-3.3977,3.3977}
Count Table 5:
---------------
h: {-2.7559,2.7559}
Count Table 6:
---------------
h: {-2.2689,2.2689}
Count Table 7:
---------------
h: {-1.7625,1.7625}
Count Table 8:
---------------
h: {-1.2562,1.2562}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-12.1962,-12.1962}
Activity(exp=1): {-12.1962,-12.1962}
Activity(exp=2): {-12.1962,-12.1962}
Activity(exp=3): {-12.1962,-12.1962}
Activity(exp=4): {-12.1962,-12.1962}
Activity(exp=5): {-12.1962,-12.1962}
Activity(exp=6): {-12.1962,-12.1962}
Activity(exp=7): {-12.1962,-12.1962}
Activity(exp=8): {-12.1962,-12.1962}
Binding mode 1:
---------------
Mononucleotide: {-1.7411,-2.1622,-2.0451,-1.7510,-1.7850,-2.0818,-2.1476,-1.6852,-1.6875,-2.1387,-2.6392,-1.2360,-2.5036,-3.5007,0.5205,-2.2176,-2.1746,-0.3656,-2.9228,-2.2384,-0.0655,-3.2246,-2.7403,-1.6711,-2.3856,-1.8002,-3.0995,-0.4162,-2.3707,-2.6891,-0.6041,-2.0375,-1.8003,-1.8763,-2.4322,-1.5907,-1.8066,-2.3461,-1.9422,-1.6047}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=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}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-0.4278,-0.4278}
Activity(exp=1): {-0.4278,-0.4278}
Activity(exp=2): {-0.4278,-0.4278}
Activity(exp=3): {-0.4278,-0.4278}
Activity(exp=4): {-0.4278,-0.4278}
Activity(exp=5): {-0.4278,-0.4278}
Activity(exp=6): {-0.4278,-0.4278}
Activity(exp=7): {-0.4278,-0.4278}
Activity(exp=8): {-0.4278,-0.4278}
Suggested variations:
key=10;6;0, description = Initial model.
> Optimizing variation "Initial model." (component1-2-variation0).
>> Starting new optimization: component1-2-variation0. (2021-05-21 23:56:16.361).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[41,42]},{"h":[43,44]},{"h":[45,46]},{"h":[47,48]},{"h":[49,50]},{"h":[51,52]},{"h":[53,54]},{"h":[55,56]},{"h":[57,58]}],"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],"activity":[[40,40],[40,40],[40,40],[40,40],[40,40],[40,40],[40,40],[40,40],[40,40]]}]}
Value and gradient before optimization:
=======================================
value = 6.053169886602143
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}
gradient norm = 1.854202837980249E-6
Already at minimum!
After: gradient norm = 1.854202837980249E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-5.8697,5.8697}
Count Table 1:
---------------
h: {-5.1770,5.1770}
Count Table 2:
---------------
h: {-4.5508,4.5508}
Count Table 3:
---------------
h: {-4.0176,4.0176}
Count Table 4:
---------------
h: {-3.3977,3.3977}
Count Table 5:
---------------
h: {-2.7559,2.7559}
Count Table 6:
---------------
h: {-2.2689,2.2689}
Count Table 7:
---------------
h: {-1.7625,1.7625}
Count Table 8:
---------------
h: {-1.2562,1.2562}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-12.1962,-12.1962}
Activity(exp=1): {-12.1962,-12.1962}
Activity(exp=2): {-12.1962,-12.1962}
Activity(exp=3): {-12.1962,-12.1962}
Activity(exp=4): {-12.1962,-12.1962}
Activity(exp=5): {-12.1962,-12.1962}
Activity(exp=6): {-12.1962,-12.1962}
Activity(exp=7): {-12.1962,-12.1962}
Activity(exp=8): {-12.1962,-12.1962}
Binding mode 1:
---------------
Mononucleotide: {-1.7411,-2.1622,-2.0451,-1.7510,-1.7850,-2.0818,-2.1476,-1.6852,-1.6875,-2.1387,-2.6392,-1.2360,-2.5036,-3.5007,0.5205,-2.2176,-2.1746,-0.3656,-2.9228,-2.2384,-0.0655,-3.2246,-2.7403,-1.6711,-2.3856,-1.8002,-3.0995,-0.4162,-2.3707,-2.6891,-0.6041,-2.0375,-1.8003,-1.8763,-2.4322,-1.5907,-1.8066,-2.3461,-1.9422,-1.6047}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=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}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-0.4278,-0.4278}
Activity(exp=1): {-0.4278,-0.4278}
Activity(exp=2): {-0.4278,-0.4278}
Activity(exp=3): {-0.4278,-0.4278}
Activity(exp=4): {-0.4278,-0.4278}
Activity(exp=5): {-0.4278,-0.4278}
Activity(exp=6): {-0.4278,-0.4278}
Activity(exp=7): {-0.4278,-0.4278}
Activity(exp=8): {-0.4278,-0.4278}
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 23:56:20.159).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[761,762]},{"h":[763,764]},{"h":[765,766]},{"h":[767,768]},{"h":[769,770]},{"h":[771,772]},{"h":[773,774]},{"h":[775,776]},{"h":[777,778]}],"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],"activity":[[760,760],[760,760],[760,760],[760,760],[760,760],[760,760],[760,760],[760,760],[760,760]],"dinucleotide":[[40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183],[184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311],[312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423],[424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519],[520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599],[600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663],[664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711],[712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743],[744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759]]}]}
Value and gradient before optimization:
=======================================
value = 8.049433766614795
gradient = 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gradient norm = 0.029004572360384492
Starting Function Value: 8.049433766614795
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 8.048886020278577 0.033997184354841 1.172131894668970 0.061501723090889
2 4 8.048009424973085 0.038797077621715 1.000000000000000 0.059805143765159
3 5 8.041535577853520 0.406685657874806 1.000000000000000 0.059288966560492
4 6 8.034358244215671 0.631751580191961 1.000000000000000 0.064199966072917
5 7 8.029842897400382 1.078958258039279 1.000000000000000 0.102234285104223
6 8 8.026202199621506 0.150884487762952 1.000000000000000 0.019842139284587
7 9 8.025342584721447 0.137018680170304 1.000000000000000 0.030333579165925
8 10 8.024125399100452 0.213994459848092 1.000000000000000 0.041117286408849
9 11 8.021960157717956 0.463609455267161 1.000000000000000 0.040917251986243
10 12 8.019270751281258 0.172663747846860 1.000000000000000 0.046651906648567
11 13 8.016562713234048 0.391833293565843 1.000000000000000 0.041455398007943
12 14 8.016114947139705 0.258387670484826 1.000000000000000 0.030762483371888
13 15 8.014946322862215 0.095322873448959 1.000000000000000 0.020741111655941
14 16 8.013413163513377 0.282561804523796 1.000000000000000 0.041495581093244
15 17 8.012350551450670 0.087416748728087 1.000000000000000 0.020062423430328
16 18 8.011376374735505 0.200272278045234 1.000000000000000 0.023395414387865
17 19 8.009438313506374 0.292877978073456 1.000000000000000 0.015839102560402
18 20 8.008300802919338 0.262812831949128 1.000000000000000 0.014939123582508
19 21 8.007040259335225 0.302897935236970 1.000000000000000 0.014806287833668
20 22 8.005782953074222 0.475734420681615 1.000000000000000 0.041182410253691
21 23 8.004932974725225 0.294195159119868 1.000000000000000 0.035551795940367
22 24 8.004297941886595 0.065461607858104 1.000000000000000 0.017626840014364
23 25 8.003903791252315 0.074576784773315 1.000000000000000 0.014436537948373
24 26 8.003628838414130 0.054956746984665 1.000000000000000 0.016238774061875
25 27 8.002689011396823 0.250311974642833 1.000000000000000 0.024288413530196
26 28 8.001771634917041 0.282362769816954 1.000000000000000 0.025149587177861
27 29 8.000678647039834 0.457222842756654 1.000000000000000 0.041115617200961
28 30 7.999722723916075 0.230972818981674 1.000000000000000 0.009198462105205
29 31 7.999575155792481 0.264979069408133 1.000000000000000 0.033548829495464
30 32 7.999330170180468 0.113960713415108 1.000000000000000 0.008797139050122
31 33 7.999250790490087 0.030017909728387 1.000000000000000 0.009810064713751
32 34 7.998983710420378 0.120260669143758 1.000000000000000 0.011454274665603
33 35 7.998531367900798 0.211170838087840 1.000000000000000 0.009491101442866
34 36 7.997963513424921 0.448078505871716 1.000000000000000 0.016007240057812
35 37 7.997562111113806 0.112803262352862 1.000000000000000 0.008286200448019
36 38 7.997382492311547 0.096918529906619 1.000000000000000 0.009240620829964
37 39 7.997115431783220 0.110933153907014 1.000000000000000 0.012307126474686
38 40 7.996813427820545 0.230497242464156 1.000000000000000 0.011593663857453
39 41 7.996692386098999 0.101304643399494 1.000000000000000 0.005806569265757
40 42 7.996609615041750 0.057568787941325 1.000000000000000 0.006874117082989
41 43 7.996515671806110 0.070114276999044 1.000000000000000 0.010335687211490
42 44 7.996392014103122 0.093299932162369 1.000000000000000 0.012084879692459
43 45 7.996123180017184 0.216757507879356 1.000000000000000 0.012535196941590
44 46 7.996005838171054 0.313396563574073 1.000000000000000 0.015079616788223
45 47 7.995743314899697 0.061831712076556 1.000000000000000 0.004640456961225
46 48 7.995671017783377 0.060643805015163 1.000000000000000 0.004117923038986
47 49 7.995582810806524 0.075620729823435 1.000000000000000 0.006843580457359
48 50 7.995487958990263 0.155643978218429 1.000000000000000 0.004290868624709
49 51 7.995424992509185 0.078107642685172 1.000000000000000 0.005138422899198
50 52 7.995367187721509 0.079495676011541 1.000000000000000 0.005192260180650
51 53 7.995311177527206 0.050771857477327 1.000000000000000 0.006225737757736
52 54 7.995233045517368 0.071998607356608 1.000000000000000 0.005200969052771
53 55 7.995146965168042 0.156183488032212 1.000000000000000 0.005966174763379
54 56 7.995097012862400 0.086613921859455 1.000000000000000 0.004268904053540
55 57 7.995068965276798 0.025026633961023 1.000000000000000 0.003299143443483
56 58 7.995029429594934 0.039922096133322 1.000000000000000 0.002066334304013
57 59 7.994995013861670 0.061320406641609 1.000000000000000 0.002845391266212
58 60 7.994947606423318 0.096885449275239 1.000000000000000 0.003422101637594
59 61 7.994897143850539 0.143159376942748 1.000000000000000 0.003384589923707
60 62 7.994891814997424 0.132719459930723 1.000000000000000 0.005551439848355
61 63 7.994850172829755 0.043389752035338 1.000000000000000 0.002331872309055
62 64 7.994835982419138 0.016495104866721 1.000000000000000 0.002138423005010
63 65 7.994809449296906 0.044483819662199 1.000000000000000 0.002995931828298
64 66 7.994777051115145 0.082891939079737 1.000000000000000 0.002275558112587
65 67 7.994753551996025 0.086004713304430 1.000000000000000 0.001995895812020
66 68 7.994730736574198 0.077975468344251 1.000000000000000 0.006172605654804
67 69 7.994712805144828 0.038996110870117 1.000000000000000 0.004785287065339
68 70 7.994688998938011 0.079266093709829 1.000000000000000 0.006536805519240
69 71 7.994673544594040 0.030121385997977 1.000000000000000 0.002947409264895
70 72 7.994660724359774 0.053579102040516 1.000000000000000 0.001611147692811
71 73 7.994652119001150 0.032564631437857 1.000000000000000 0.001805029563369
72 74 7.994640508591250 0.062929872591270 1.000000000000000 0.002579424563678
73 75 7.994624815206989 0.054574859139280 1.000000000000000 0.003312194585851
74 76 7.994587734473614 0.152463468533292 1.000000000000000 0.002141762992385
75 77 7.994559439293738 0.084731233960006 1.000000000000000 0.003603432567894
76 78 7.994536317403134 0.100017536403967 1.000000000000000 0.005992865348219
77 79 7.994509203375774 0.091244672353158 1.000000000000000 0.003213795778942
78 80 7.994484111719106 0.033309124196724 1.000000000000000 0.005521591864146
79 81 7.994426967028286 0.105352221725382 1.000000000000000 0.012399894702430
80 82 7.994401402428009 0.024447566128284 1.000000000000000 0.008779794388233
81 83 7.994352183051587 0.172926503975258 1.000000000000000 0.012996630888263
82 84 7.994280729414280 0.062870903184803 1.000000000000000 0.009603319596519
83 85 7.994210255016196 0.077707172774803 1.000000000000000 0.010952447609862
84 87 7.994079878663417 0.160665582730711 0.336864060590526 0.005531025558939
85 88 7.993947207878451 0.227417761223071 1.000000000000000 0.020889478103381
86 89 7.993918047581515 0.137572441181233 1.000000000000000 0.017055852532940
87 90 7.993799115344610 0.059615417513843 1.000000000000000 0.008057291336330
88 91 7.993716426978409 0.104000946316802 1.000000000000000 0.012857949122058
89 92 7.993647225083728 0.034088124781992 1.000000000000000 0.012498235982529
90 93 7.993372137337579 0.131607138054133 1.000000000000000 0.016619547488835
91 94 7.993128220330812 0.136522431156489 1.000000000000000 0.010533994548512
92 95 7.992990817128407 0.126088683237856 1.000000000000000 0.007936141831035
93 96 7.992834801808899 0.074124297657241 1.000000000000000 0.008428214912636
94 97 7.992746239247280 0.038757283465028 1.000000000000000 0.007316661262474
95 98 7.992465772268979 0.178224485285226 1.000000000000000 0.006967953424287
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343 359 7.991383083864863 0.044416925575977 1.000000000000000 0.000556739315438
344 360 7.991382932801493 0.052810446592248 1.000000000000000 0.000445321085692
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405 424 7.991365805851022 0.086309130190461 1.000000000000000 0.000269368719683
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437 457 7.991359686668006 0.008170577664096 1.000000000000000 0.000054360947701
438 458 7.991359655991005 0.010769627393215 1.000000000000000 0.000043255535047
439 459 7.991359639245181 0.006357258064494 1.000000000000000 0.000093360367282
440 460 7.991359627530551 0.002740655680839 1.000000000000000 0.000054813339731
441 461 7.991359614411159 0.002461354058482 1.000000000000000 0.000040469033853
442 462 7.991359603452778 0.003026446782725 1.000000000000000 0.000078136679451
443 463 7.991359590795772 0.002335375745870 1.000000000000000 0.000068541437274
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448 468 7.991359551154812 0.001365800019279 1.000000000000000 0.000022412410303
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450 471 7.991359538862517 0.003787618621170 0.498551525898746 0.000039746732020
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456 477 7.991359518895367 0.001502814046959 1.000000000000000 0.000021960431952
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474 497 7.991359504530196 0.000512363759798 1.000000000000000 0.000006181748571
475 498 7.991359504335835 0.000759682354459 1.000000000000000 0.000005590695659
476 499 7.991359504209938 0.000324454478522 1.000000000000000 0.000004596510193
477 500 7.991359504054218 0.000294638807951 1.000000000000000 0.000004661754922
478 501 7.991359503826010 0.000751321068490 1.000000000000000 0.000005535529878
479 503 7.991359503773046 0.000213141406875 0.229571620666860 0.000005386558666
480 504 7.991359503658487 0.000766136593845 1.000000000000000 0.000003603353268
481 505 7.991359503553881 0.000227972725959 1.000000000000000 0.000002646146724
482 506 7.991359503416771 0.000261473985707 1.000000000000000 0.000002891012625
483 507 7.991359503368115 0.000588556354319 1.000000000000000 0.000007281342615
484 508 7.991359503294634 0.000101404093680 1.000000000000000 0.000002991788014
485 509 7.991359503257968 0.000088572054504 1.000000000000000 0.000002295689636
486 510 7.991359503206230 0.000341120364421 1.000000000000000 0.000002726294998
487 511 7.991359503175522 0.000582719334020 1.000000000000000 0.000004317159128
488 512 7.991359503137889 0.000153140290584 1.000000000000000 0.000002313974886
489 513 7.991359503110566 0.000057599298762 1.000000000000000 0.000001850476185
490 514 7.991359503086160 0.000058958978902 1.000000000000000 0.000001743842787
491 515 7.991359503053315 0.000085065677400 1.000000000000000 0.000001692559300
492 516 7.991359503016652 0.000645019320765 1.000000000000000 0.000002076099924
493 517 7.991359503006695 0.000186406789152 1.000000000000000 0.000003950466034
494 518 7.991359502980121 0.000186406789152 1.000000000000000 0.000001243514710
Convergence criteria met.
After: gradient norm = 1.2435147103720751E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-5.5693,5.5693}
Count Table 1:
---------------
h: {-4.8764,4.8764}
Count Table 2:
---------------
h: {-4.2509,4.2509}
Count Table 3:
---------------
h: {-3.7169,3.7169}
Count Table 4:
---------------
h: {-3.0865,3.0865}
Count Table 5:
---------------
h: {-2.4360,2.4360}
Count Table 6:
---------------
h: {-1.9591,1.9591}
Count Table 7:
---------------
h: {-1.4654,1.4654}
Count Table 8:
---------------
h: {-0.9839,0.9839}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-12.1962,-12.1962}
Activity(exp=1): {-12.1962,-12.1962}
Activity(exp=2): {-12.1962,-12.1962}
Activity(exp=3): {-12.1962,-12.1962}
Activity(exp=4): {-12.1962,-12.1962}
Activity(exp=5): {-12.1962,-12.1962}
Activity(exp=6): {-12.1962,-12.1962}
Activity(exp=7): {-12.1962,-12.1962}
Activity(exp=8): {-12.1962,-12.1962}
Binding mode 1:
---------------
Mononucleotide: {-0.7148,-0.8872,-0.7862,-0.6702,-0.7375,-0.8519,-0.7420,-0.7271,-0.7075,-0.9281,-0.7825,-0.6403,-0.7391,-1.0675,-0.4738,-0.7780,-0.7333,-0.8029,-0.8815,-0.6407,-0.6924,-0.8068,-0.7753,-0.7838,-0.8561,-0.8514,-0.7999,-0.5510,-0.8035,-0.8626,-0.6937,-0.6986,-0.7385,-0.8141,-0.8076,-0.6982,-0.7843,-0.9268,-0.6925,-0.6547}
Dinucleotide(d=1): {-0.1199,-0.1695,-0.2553,-0.1667,-0.1370,-0.2840,-0.3098,-0.1548,-0.3171,-0.1351,-0.0865,-0.2566,-0.1656,-0.2584,-0.0994,-0.1429,-0.1315,-0.2261,-0.2167,-0.1554,-0.0830,-0.2999,-0.1798,-0.2916,-0.3570,-0.1332,-0.1557,-0.1043,-0.1499,-0.2597,-0.2254,-0.0896,0.0130,-0.1729,-0.1939,-0.3477,-0.3412,-0.4638,-0.1690,0.0258,-0.0915,-0.1669,-0.1982,-0.2986,-0.3469,-0.2330,0.1038,-0.1778,0.3256,-0.9231,-0.0558,-0.1694,-0.3880,-0.5557,-0.1138,0.1624,-0.5967,0.6749,-0.2879,-0.5447,-0.0209,-0.5145,-0.1294,0.0784,-0.2610,0.0031,-0.0327,-0.3083,0.4289,-0.8529,-0.6468,-0.0708,-0.5097,-0.0214,-0.0775,-0.1638,-0.4947,0.0077,0.0249,-0.0839,-0.4928,0.0371,-0.3972,0.1705,-0.7424,-0.4645,0.0729,0.2048,0.0087,-0.0739,-0.1753,-0.4208,0.2361,-0.2611,-0.1989,-0.5619,-0.1115,-0.0367,-0.5788,-0.1127,-0.1114,-0.6218,-0.0871,-0.0326,0.0198,-0.2500,-0.3328,-0.1731,-0.5988,0.0317,0.2303,-0.2931,-0.0234,-0.4938,-0.0735,-0.2268,-0.2588,-0.3391,-0.1856,-0.0491,-0.3001,0.2003,-0.3657,-0.2873,-0.1292,-0.2724,-0.1536,-0.1007,-0.0558,-0.3340,-0.1259,-0.2199,-0.1683,-0.2487,-0.2211,-0.1539,-0.4651,-0.1053,-0.0280,-0.2374,-0.1215,-0.2221,-0.3193,-0.0325}
Dinucleotide(d=2): {-0.2163,-0.1627,-0.1351,-0.1981,-0.1743,-0.2455,-0.3002,-0.1636,-0.1257,-0.3326,-0.1448,-0.1918,-0.1909,-0.1840,-0.2092,-0.0840,-0.0865,-0.3923,-0.1007,-0.1662,-0.1659,-0.3833,-0.0252,-0.2906,-0.1834,-0.1290,-0.2625,-0.1515,-0.3170,-0.1560,-0.0730,-0.1754,-0.1621,-0.0719,-0.3420,-0.0786,-0.2284,-0.0684,-0.1484,-0.4333,0.0173,-0.8057,-0.0076,-0.1104,-0.3133,0.0251,-0.3417,0.0105,-0.2581,0.1648,-0.2611,-0.3248,-0.4499,-0.2698,0.0381,-0.2708,0.4431,-0.4325,-0.6397,-0.0269,-0.6204,-0.2063,0.0909,-0.0353,-0.0655,-0.2030,-0.4087,0.0089,-0.3312,-0.0501,-0.7521,0.2048,-0.1773,-0.1350,-0.0867,-0.3891,-0.1866,-0.3791,0.2732,-0.3813,-0.2177,-0.5657,0.3135,-0.3491,-0.3005,0.1224,-0.5084,-0.1332,-0.0483,-0.3047,-0.3474,-0.0237,-0.1612,-0.1430,-0.2652,-0.1264,-0.2323,-0.3958,-0.0929,-0.1465,-0.1966,-0.2818,-0.2383,-0.1274,-0.1187,-0.1989,-0.1835,-0.2956,-0.1766,0.0308,-0.2849,-0.1196,-0.2226,-0.2628,-0.1306,-0.1798,-0.2242,-0.1543,-0.3997,-0.0942,-0.1279,-0.2542,-0.0373,-0.2800,-0.2034,-0.2400,-0.1488,-0.0987}
Dinucleotide(d=3): {-0.1229,-0.3693,-0.0389,-0.2038,-0.2324,-0.2584,-0.1975,-0.1864,-0.2426,-0.2737,-0.0742,-0.1989,-0.1566,-0.1511,-0.1531,-0.1988,-0.1475,-0.2326,-0.2878,-0.0593,-0.2960,-0.0634,-0.3573,-0.1353,-0.1422,-0.3412,0.0431,-0.3266,-0.1337,-0.1632,-0.3042,-0.1115,-0.0956,-0.3901,-0.0192,-0.1928,-0.0563,-0.2882,-0.3118,-0.2358,-0.3661,0.1687,-0.4317,-0.2216,-0.1492,-0.3544,-0.0254,-0.0892,-0.3260,-0.2426,0.0567,-0.2232,-0.1994,-0.3442,-0.1315,-0.3234,-0.0958,-0.0325,-0.6750,0.2113,-0.1836,-0.1935,-0.1259,-0.2301,-0.1105,-0.2064,-0.2283,-0.1449,-0.3627,-0.3016,0.1962,-0.4153,-0.1523,-0.0833,-0.4204,-0.2033,-0.1475,-0.2313,-0.3056,0.0586,-0.0432,-0.3418,-0.0834,-0.2108,-0.4143,0.0776,-0.4301,-0.0950,-0.0296,-0.2739,-0.2237,-0.2281,-0.2635,-0.2961,-0.0720,-0.1309,-0.1501,-0.5174,-0.0844,-0.1399,-0.2066,-0.1951,-0.3161,-0.1237,-0.1688,-0.2145,-0.1093,-0.3004,-0.2424,-0.0304,-0.1781,-0.0814}
Dinucleotide(d=4): {-0.0823,-0.2142,-0.2541,-0.1555,-0.4007,-0.0729,-0.3389,-0.0943,-0.1409,-0.2561,-0.0816,-0.3071,-0.1234,-0.2550,-0.2033,-0.0784,-0.1113,-0.2811,-0.1017,-0.2445,-0.1411,-0.1460,-0.3637,-0.2027,-0.1889,-0.1228,-0.2801,-0.1459,-0.2426,-0.2539,-0.0506,-0.1816,-0.2283,-0.1456,-0.2261,-0.0751,-0.3344,-0.1162,-0.4312,-0.0451,-0.1793,-0.4883,0.1244,-0.3006,-0.0890,-0.1081,-0.3197,-0.0963,-0.1910,-0.1331,-0.3750,-0.0493,-0.2188,-0.2133,-0.3951,-0.1971,-0.2546,-0.2313,0.2297,-0.2636,-0.1065,-0.2472,-0.2513,-0.1613,-0.1371,-0.1962,-0.1771,-0.2219,-0.2675,-0.1435,-0.2564,-0.1395,-0.1431,-0.3028,-0.2844,-0.1539,-0.1905,-0.1724,-0.0947,-0.1778,-0.0523,-0.2497,-0.1635,-0.2198,-0.2965,-0.0350,-0.2299,-0.2485,-0.2520,-0.3096,-0.1921,-0.0274,-0.1882,-0.3393,-0.0977,-0.1571}
Dinucleotide(d=5): {-0.0724,-0.2312,-0.2141,-0.2009,-0.2441,-0.1498,-0.2676,-0.2204,-0.1893,-0.2711,-0.0884,-0.2435,-0.1868,-0.1536,-0.2081,-0.1176,-0.1366,-0.1962,-0.3576,-0.0477,-0.4395,-0.2370,0.0305,-0.2352,-0.1585,-0.2266,-0.1681,-0.1659,-0.1322,-0.1723,-0.3365,-0.0794,-0.0990,-0.2228,-0.2042,-0.1784,-0.2891,-0.1373,-0.2776,-0.2144,-0.3444,-0.2755,-0.0405,-0.1429,-0.0864,-0.2185,-0.1748,-0.1531,-0.2471,-0.1815,-0.0743,-0.2526,-0.2689,-0.2569,-0.2647,-0.2459,-0.0502,-0.1309,-0.3142,0.0142,-0.1722,-0.2339,-0.1565,-0.2231,-0.1922,-0.2253,-0.1499,-0.1499,-0.1046,-0.1486,-0.4558,-0.1153,-0.3122,-0.2687,-0.0106,-0.2987,-0.1699,-0.2624,-0.1108,-0.0836}
Dinucleotide(d=6): {-0.2330,-0.2440,-0.0234,-0.2189,-0.3505,-0.2298,-0.2523,-0.0594,-0.0945,-0.2397,-0.3039,-0.1491,-0.1845,-0.1321,-0.2364,-0.1073,-0.1361,-0.2280,-0.2072,-0.1655,-0.2788,-0.2154,-0.2329,-0.1251,-0.2484,-0.1978,-0.1099,-0.1875,-0.1456,-0.2162,-0.1449,-0.2195,-0.1193,-0.2534,-0.1812,-0.1566,-0.2993,-0.1875,-0.2643,-0.1714,-0.1830,-0.1260,-0.2605,-0.2167,-0.1408,-0.2463,-0.1044,-0.1480,-0.1569,-0.1561,-0.1714,-0.2663,-0.3250,-0.2984,-0.2930,-0.1330,-0.1192,-0.1218,-0.0532,-0.1620,-0.1858,-0.3493,-0.1786,-0.0887}
Dinucleotide(d=7): {-0.1808,-0.1880,-0.2017,-0.1437,-0.2362,-0.2624,-0.1214,-0.2677,-0.2350,-0.2514,-0.1669,-0.1364,-0.1519,-0.1592,-0.2026,-0.1534,-0.1618,-0.2097,-0.1275,-0.2386,-0.2195,-0.1674,-0.2951,-0.1690,-0.1406,-0.2652,-0.2257,-0.1145,-0.2153,-0.1706,-0.1633,-0.1749,-0.1574,-0.2699,-0.1477,-0.1327,-0.2919,-0.2114,-0.3091,-0.1129,-0.1927,-0.2173,-0.0720,-0.3102,-0.1438,-0.2144,-0.1716,-0.1037}
Dinucleotide(d=8): {-0.2086,-0.1902,-0.1236,-0.1937,-0.1956,-0.2345,-0.2805,-0.1739,-0.1484,-0.2051,-0.2700,-0.1668,-0.1845,-0.1819,-0.1410,-0.1603,-0.1758,-0.2394,-0.1652,-0.1580,-0.2281,-0.2298,-0.1940,-0.1968,-0.1998,-0.2483,-0.1403,-0.1561,-0.1845,-0.2030,-0.1957,-0.1437}
Dinucleotide(d=9): {-0.1771,-0.2333,-0.1547,-0.1505,-0.2328,-0.2825,-0.2329,-0.1382,-0.2274,-0.1951,-0.1318,-0.2343,-0.1506,-0.2094,-0.1757,-0.1324}
Activity(exp=0): {-0.1700,-0.1700}
Activity(exp=1): {-0.1700,-0.1700}
Activity(exp=2): {-0.1700,-0.1700}
Activity(exp=3): {-0.1700,-0.1700}
Activity(exp=4): {-0.1700,-0.1700}
Activity(exp=5): {-0.1700,-0.1700}
Activity(exp=6): {-0.1700,-0.1700}
Activity(exp=7): {-0.1700,-0.1700}
Activity(exp=8): {-0.1700,-0.1700}
> Optimizing the full model (component1-4-all).
>> Starting new optimization: component1-4-all. (2021-05-22 02:04:02.261).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{},{},{},{}],"countTable":[{"h":[779,780]},{"h":[781,782]},{"h":[783,784]},{"h":[785,786]},{"h":[787,788]},{"h":[789,790]},{"h":[791,792]},{"h":[793,794]},{"h":[795,796]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11],[12,13],[14,15],[16,17]]},{"mononucleotide":[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],"activity":[[778,778],[778,778],[778,778],[778,778],[778,778],[778,778],[778,778],[778,778],[778,778]],"dinucleotide":[[58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201],[202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329],[330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441],[442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537],[538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617],[618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681],[682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729],[730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761],[762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777]]}]}
Value and gradient before optimization:
=======================================
value = 7.991359502995264
gradient = 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gradient norm = 0.027205969789981944
Starting Function Value: 7.991359502995264
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 7.979616249062844 1.000000000000000 36.756638624520930 0.120222250696984
2 3 7.964763685870976 0.737928337756145 1.000000000000000 0.235413908260804
3 4 7.942713937229408 1.516862874379864 1.000000000000000 0.209243087695927
4 5 7.928989033186054 0.869128534838189 1.000000000000000 0.216577080682777
5 6 7.911414789448655 2.660003431918281 1.000000000000000 0.403683334795215
6 7 7.889439208645269 0.194705883965521 1.000000000000000 0.084538377264277
7 8 7.886809137044981 0.154683192075314 1.000000000000000 0.026678785597169
8 9 7.882522846190252 1.365091750065985 1.000000000000000 0.057015919551544
9 10 7.880354850859397 0.534485217630961 1.000000000000000 0.024185504800776
10 11 7.879527676816944 0.397765667723943 1.000000000000000 0.017445262656846
11 12 7.878848834034429 0.408603095442205 1.000000000000000 0.013989200736291
12 13 7.878415567002154 0.325633298561764 1.000000000000000 0.012203646962862
13 14 7.877932615456636 0.231269750474596 1.000000000000000 0.013692548636679
14 15 7.876932946595828 0.381619621796720 1.000000000000000 0.020124300912229
15 16 7.875991041396111 0.315887159263979 1.000000000000000 0.013482697245655
16 17 7.875733400027560 0.202585164097156 1.000000000000000 0.023253591763544
17 18 7.875334731812030 0.076756686589488 1.000000000000000 0.007871378844638
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982 1010 7.867763633835583 0.016410930579900 1.000000000000000 0.000033207868502
983 1011 7.867763626709824 0.017555666325699 1.000000000000000 0.000051874240565
984 1012 7.867763620329628 0.023731775043610 1.000000000000000 0.000043162012179
985 1013 7.867763616805085 0.010547709017408 1.000000000000000 0.000043192969784
986 1014 7.867763611141601 0.009787032362884 1.000000000000000 0.000027323130291
987 1015 7.867763607057730 0.010458880039381 1.000000000000000 0.000032408707123
988 1016 7.867763600878902 0.014616095798899 1.000000000000000 0.000038259717789
989 1017 7.867763594550503 0.014230410947435 1.000000000000000 0.000039052828255
990 1018 7.867763588847865 0.017344378252058 1.000000000000000 0.000029348473572
991 1019 7.867763584872826 0.004671897030399 1.000000000000000 0.000022089365047
992 1020 7.867763581712559 0.016168973165582 1.000000000000000 0.000029356570006
993 1021 7.867763579991204 0.002430134298956 1.000000000000000 0.000044426194516
994 1022 7.867763577455056 0.001085100648030 1.000000000000000 0.000020988755180
995 1023 7.867763574345635 0.006019883032074 1.000000000000000 0.000024337364558
996 1024 7.867763571645742 0.004436370485546 1.000000000000000 0.000027362347523
997 1025 7.867763566556268 0.011849529556497 1.000000000000000 0.000032235116438
998 1026 7.867763565163720 0.016924884078235 1.000000000000000 0.000063768845721
999 1027 7.867763559738251 0.004572395854843 1.000000000000000 0.000019955413519
1000 1028 7.867763557690640 0.008262073371718 1.000000000000000 0.000017536866057
>>> Maximum iteration count reached.
After: gradient norm = 1.7536866057342706E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.3056,0.3056}
Count Table 1:
---------------
h: {-0.1150,0.1150}
Count Table 2:
---------------
h: {-0.0392,0.0392}
Count Table 3:
---------------
h: {-2.0176,2.0176}
Count Table 4:
---------------
h: {-2.3292,2.3292}
Count Table 5:
---------------
h: {-2.1385,2.1385}
Count Table 6:
---------------
h: {-1.7666,1.7666}
Count Table 7:
---------------
h: {-1.3013,1.3013}
Count Table 8:
---------------
h: {-0.8560,0.8560}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0317,0.1713}
Activity(exp=1): {0.0317,-0.0339}
Activity(exp=2): {0.0317,-0.1339}
Activity(exp=3): {0.0317,-7.7810}
Activity(exp=4): {0.0317,-10.0276}
Activity(exp=5): {0.0317,-12.6417}
Activity(exp=6): {0.0317,-16.3451}
Activity(exp=7): {0.0317,-15.6137}
Activity(exp=8): {0.0317,-16.6151}
Binding mode 1:
---------------
Mononucleotide: {-0.7233,-0.8467,-0.7611,-0.6569,-0.8092,-0.7415,-0.7740,-0.6633,-0.7767,-0.8829,-0.7282,-0.6003,-0.8208,-0.9997,-0.4123,-0.7552,-0.7991,-0.6406,-0.9457,-0.6026,-0.5072,-0.9690,-0.8289,-0.6829,-0.8218,-0.7582,-0.7526,-0.6554,-0.8300,-0.8740,-0.6953,-0.5887,-0.7577,-0.8005,-0.7423,-0.6874,-0.7650,-0.9497,-0.6435,-0.6299}
Dinucleotide(d=1): {-0.1455,-0.1339,-0.2371,-0.1963,-0.1411,-0.2764,-0.3356,-0.0952,-0.3821,-0.0583,-0.1109,-0.2263,-0.1447,-0.2763,-0.0947,-0.1338,-0.1616,-0.2178,-0.2838,-0.1345,-0.0432,-0.2781,-0.1598,-0.2619,-0.4359,-0.1155,-0.1754,-0.0690,-0.1626,-0.2598,-0.1047,-0.1243,0.0757,-0.5693,-0.0053,-0.3133,-0.4084,-0.0027,-0.2663,-0.1525,-0.1306,-0.0949,-0.4713,-0.0012,-0.3586,-0.3262,0.2804,-0.2433,0.2445,-0.9800,-0.1087,-0.0289,-0.1930,-0.3302,-0.2320,0.0489,-0.6881,0.7438,-0.2850,-0.5515,-0.0546,-0.6946,-0.0072,0.1286,0.0439,-0.3847,-0.1485,-0.2610,0.2786,-0.4137,-0.6257,-0.0213,-0.4169,-0.1582,-0.1241,-0.1612,-0.5144,0.0325,0.0486,-0.1619,-0.5130,0.0614,-0.4175,0.3338,-0.4525,-0.8159,0.2091,0.0019,-0.0999,0.1249,-0.2870,-0.4665,0.2564,-0.1668,-0.1645,-0.5919,-0.1549,0.2080,-0.7932,-0.0549,0.0742,-0.9616,-0.0727,0.1416,-0.0047,0.1430,-0.5670,-0.1863,-0.6016,-0.3933,0.4974,-0.2622,-0.0910,-0.4297,-0.0858,-0.1825,-0.1760,-0.5143,-0.0851,-0.0766,-0.3587,0.3044,-0.5063,-0.2622,-0.0757,-0.3040,-0.0498,-0.0948,-0.0675,-0.2968,-0.1226,-0.2546,-0.0858,-0.3493,-0.2167,-0.1336,-0.5403,-0.0483,-0.0144,-0.1868,-0.1154,-0.2395,-0.2799,-0.0365}
Dinucleotide(d=2): {-0.2686,-0.1972,-0.0916,-0.1638,-0.2106,-0.1500,-0.3140,-0.1663,-0.1294,-0.3536,-0.0817,-0.2070,-0.1657,-0.1798,-0.2538,-0.0548,-0.0740,-0.8476,0.1092,-0.1497,-0.1738,0.0806,-0.2428,-0.3864,-0.2114,-0.2496,-0.1206,-0.1206,-0.3175,-0.1166,-0.0966,-0.0704,-0.2113,-0.0053,-0.3278,-0.1571,-0.3053,0.0236,-0.1783,-0.3585,0.0600,-0.9348,-0.0146,-0.0206,-0.2888,0.0807,-0.3484,-0.0013,-0.2267,-0.0209,-0.1400,-0.3267,-0.4326,-0.0551,-0.1975,-0.1939,0.4773,-0.3184,-0.6481,-0.1050,-0.4992,-0.4898,0.1445,0.0442,-0.0124,-0.1531,-0.3464,-0.1561,-0.3359,-0.0516,-0.8146,0.3662,-0.1381,-0.0389,-0.0545,-0.6566,-0.1943,-0.3869,0.3057,-0.3204,-0.1763,-0.4934,0.3983,-0.3649,-0.4082,0.0132,-0.5832,0.0001,-0.0406,-0.3213,-0.3651,-0.0426,-0.1284,-0.0401,-0.3349,-0.1007,-0.2417,-0.3134,-0.0782,-0.1912,-0.1675,-0.3173,-0.1448,-0.1296,-0.1450,-0.1157,-0.2444,-0.2442,-0.1952,-0.0677,-0.2765,-0.1155,-0.2474,-0.2873,-0.0937,-0.2010,-0.2010,-0.2374,-0.3762,-0.0685,-0.1271,-0.2423,-0.0584,-0.2735,-0.1862,-0.1639,-0.1346,-0.0894}
Dinucleotide(d=3): {-0.0167,-0.7991,0.1194,-0.1656,-0.3607,0.1254,-0.2696,-0.3390,-0.1804,-0.3582,-0.0833,-0.0824,-0.2300,-0.1024,-0.1194,-0.1260,-0.1741,-0.2029,-0.3088,-0.0939,-0.2848,0.0784,-0.4783,-0.1026,-0.2270,-0.3759,0.0720,-0.2601,-0.0903,-0.1579,-0.2657,-0.1162,-0.0401,-0.5474,-0.0255,-0.1769,0.0443,-0.4114,-0.2908,-0.2059,-0.2228,0.1394,-0.5850,-0.1219,-0.2378,-0.2091,0.0232,-0.1204,-0.3060,-0.3230,0.1836,-0.3977,-0.2154,0.0093,-0.3450,-0.3812,0.0224,-0.1808,-0.6732,0.3052,-0.2434,-0.1824,-0.0131,-0.2472,-0.1668,-0.4368,-0.1753,-0.0024,-0.2888,-0.1201,0.2213,-0.5408,-0.1738,-0.1335,-0.4942,-0.1103,-0.1380,-0.1439,-0.3258,0.0413,-0.0111,-0.3085,0.0200,-0.1958,-0.4111,0.0259,-0.4926,-0.1310,-0.0676,-0.2609,-0.2620,-0.2204,-0.2768,-0.2501,-0.0446,-0.1015,-0.1542,-0.4448,-0.0732,-0.1690,-0.1806,-0.2229,-0.2513,-0.0946,-0.1596,-0.0998,-0.1704,-0.3196,-0.2644,-0.1878,-0.1434,-0.0525}
Dinucleotide(d=4): {-0.0979,-0.1886,-0.2423,-0.1773,-0.3804,0.0138,-0.4290,-0.0948,-0.2001,-0.2554,-0.0510,-0.2453,-0.1269,-0.2131,-0.2279,-0.0719,-0.0408,-0.4157,-0.1540,-0.2119,-0.1733,-0.0367,-0.3703,-0.1684,-0.0684,-0.2476,-0.2467,-0.2008,-0.2067,-0.2783,-0.0711,-0.0972,-0.2325,-0.1216,-0.2859,-0.0984,-0.2380,-0.0385,-0.5001,-0.1093,-0.2840,-0.4616,0.2044,-0.2669,-0.0316,-0.1333,-0.2569,-0.1338,-0.1506,-0.3397,-0.3067,-0.0031,-0.3221,-0.0815,-0.5718,-0.0316,-0.2311,-0.0627,0.2707,-0.4338,-0.0700,-0.3492,-0.2084,-0.0965,-0.1500,-0.2583,-0.1486,-0.2424,-0.1789,-0.0781,-0.3092,-0.0844,-0.2163,-0.3864,-0.1625,-0.1771,-0.2018,-0.0963,-0.1208,-0.1768,0.0132,-0.2094,-0.1279,-0.1753,-0.3112,-0.1440,-0.2226,-0.2763,-0.3078,-0.2954,-0.1953,-0.0466,-0.1850,-0.2829,-0.0903,-0.1313}
Dinucleotide(d=5): {-0.0568,-0.2766,-0.2427,-0.1540,-0.1830,-0.1682,-0.3249,-0.1675,-0.1037,-0.3042,-0.1248,-0.2339,-0.1533,-0.2102,-0.1502,-0.1341,-0.1687,-0.2057,-0.3419,-0.0921,-0.3370,-0.1609,-0.0107,-0.2469,-0.2107,-0.2251,-0.1073,-0.2199,-0.1024,-0.1534,-0.3167,-0.0887,-0.1439,-0.2806,-0.2135,-0.1327,-0.2495,-0.1035,-0.3579,-0.1699,-0.3302,-0.2718,0.0232,-0.1734,-0.1073,-0.2104,-0.1723,-0.0945,-0.2453,-0.2319,-0.0254,-0.3253,-0.4161,-0.1492,-0.1459,-0.2711,0.0329,-0.1145,-0.4247,0.0742,-0.1450,-0.2748,-0.1503,-0.1755,-0.1561,-0.3304,-0.1667,-0.1248,-0.0444,-0.0467,-0.4844,-0.0926,-0.3577,-0.3635,0.0779,-0.3289,-0.1985,-0.1917,-0.1128,-0.0667}
Dinucleotide(d=6): {-0.2461,-0.2544,-0.0004,-0.2350,-0.2679,-0.1453,-0.3514,-0.0889,-0.1605,-0.2168,-0.1873,-0.1869,-0.1400,-0.1357,-0.2350,-0.1365,-0.1927,-0.2901,-0.1965,-0.1284,-0.2770,-0.0912,-0.2615,-0.1189,-0.2112,-0.2248,-0.1321,-0.2015,-0.1487,-0.2721,-0.1097,-0.1314,-0.1465,-0.2808,-0.1697,-0.1815,-0.3008,-0.1651,-0.2253,-0.1869,-0.1712,-0.1068,-0.2871,-0.1684,-0.1403,-0.2490,-0.0662,-0.1426,-0.1462,-0.2912,-0.1058,-0.2919,-0.2958,-0.2379,-0.3143,-0.1376,-0.1133,-0.0420,-0.0756,-0.1499,-0.2069,-0.3819,-0.1487,-0.0490}
Dinucleotide(d=7): {-0.1736,-0.1848,-0.2133,-0.1508,-0.2348,-0.2373,-0.1753,-0.1954,-0.2250,-0.2849,-0.1290,-0.1292,-0.1972,-0.1672,-0.1812,-0.1090,-0.1728,-0.2180,-0.1462,-0.2700,-0.2260,-0.1042,-0.2479,-0.1648,-0.1391,-0.2981,-0.2314,-0.1109,-0.2165,-0.1831,-0.1172,-0.1418,-0.1941,-0.3043,-0.1552,-0.1204,-0.2494,-0.1863,-0.3255,-0.1149,-0.2038,-0.2137,0.0095,-0.3408,-0.1135,-0.2244,-0.1887,-0.0624}
Dinucleotide(d=8): {-0.2246,-0.1806,-0.1113,-0.2092,-0.2088,-0.2011,-0.2474,-0.1854,-0.1428,-0.2282,-0.2612,-0.1335,-0.1807,-0.1875,-0.1288,-0.1568,-0.2009,-0.2879,-0.1648,-0.1562,-0.1927,-0.1779,-0.1965,-0.1714,-0.2069,-0.2504,-0.1001,-0.2196,-0.1679,-0.2240,-0.1848,-0.0860}
Dinucleotide(d=9): {-0.1731,-0.2192,-0.1560,-0.1744,-0.2332,-0.2852,-0.1983,-0.1310,-0.2120,-0.2057,-0.1334,-0.2107,-0.1525,-0.2296,-0.1576,-0.1162}
Activity(exp=0): {-0.1468,-0.1468}
Activity(exp=1): {-0.1468,-0.1468}
Activity(exp=2): {-0.1468,-0.1468}
Activity(exp=3): {-0.1468,-0.1468}
Activity(exp=4): {-0.1468,-0.1468}
Activity(exp=5): {-0.1468,-0.1468}
Activity(exp=6): {-0.1468,-0.1468}
Activity(exp=7): {-0.1468,-0.1468}
Activity(exp=8): {-0.1468,-0.1468}
> Optimization done.
Probound Model
±
Optimized model:
{"metadata":{"timeStamp":"2021-05-22 06:16:55.218","logLikelihoodPerRead":7.86776355769064,"logLikelihood":1160754.8702365882,"gradientCalls":1872,"fitSteps":1791,"regularization":2.0639892065076992,"functionCalls":0,"fitter":"proBound","fitName":"component1-4-all","fitTime":23319.753,"dataLoops":1872},"optimizerSetting":{"output":{"outputPath":"jobs/c9b263b23beb","baseName":"fit"},"nThreads":20,"likelihoodThreshold":0,"lbfgsSettings":{"memory":100,"convergence":1.0E-7,"MCSearch":true,"maxIters":1000},"lambdaL2":1.0E-6,"fixedLibrarySize":false,"expBound":40,"nRetries":3,"hkSettings":{"epsilon":1.0E-7,"kickFinal":false,"fdDelta":1.0E-4,"kickAll":false,"maxIters":200,"evCutoff":1.0E-9}},"modelSettings":{"enrichmentModel":[{"variationsOptimized":false,"bindingSaturation":true,"cumulativeEnrichment":true,"concentration":1,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 0","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1],"variationDescription":[],"modifications":[]},{"variationsOptimized":false,"bindingSaturation":true,"cumulativeEnrichment":true,"concentration":4,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 1","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1],"variationDescription":[],"modifications":[]},{"variationsOptimized":false,"bindingSaturation":true,"cumulativeEnrichment":true,"concentration":14,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 2","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1],"variationDescription":[],"modifications":[]},{"variationsOptimized":false,"bindingSaturation":true,"cumulativeEnrichment":true,"concentration":40,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 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8","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1],"variationDescription":[],"modifications":[]}],"letterOrder":"ACGT","countTable":[{"leftFlank":"GGGGAGTTCTACAGTCCGACGATC","variationsOptimized":true,"transliterate":{"in":[],"out":[]},"variableRegionLength":40,"countTableFile":"jobs/c9b263b23beb/countTable.0.tsv.gz","modeledColumns":[0,1],"inputFileType":"tsv.gz","nColumns":2,"rightFlank":"TGGAATTCTCGGGTGTCAAGG","componentName":"Count table 0","freezingLevel":0,"includeComponent":true,"variationDescription":[]},{"leftFlank":"GGGGAGTTCTACAGTCCGACGATC","variationsOptimized":true,"transliterate":{"in":[],"out":[]},"variableRegionLength":40,"countTableFile":"jobs/c9b263b23beb/countTable.1.tsv.gz","modeledColumns":[0,1],"inputFileType":"tsv.gz","nColumns":2,"rightFlank":"TGGAATTCTCGGGTGTCAAGG","componentName":"Count table 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5","freezingLevel":0,"includeComponent":true,"variationDescription":[]},{"leftFlank":"GGGGAGTTCTACAGTCCGACGATC","variationsOptimized":true,"transliterate":{"in":[],"out":[]},"variableRegionLength":40,"countTableFile":"jobs/c9b263b23beb/countTable.6.tsv.gz","modeledColumns":[0,1],"inputFileType":"tsv.gz","nColumns":2,"rightFlank":"TGGAATTCTCGGGTGTCAAGG","componentName":"Count table 6","freezingLevel":0,"includeComponent":true,"variationDescription":[]},{"leftFlank":"GGGGAGTTCTACAGTCCGACGATC","variationsOptimized":true,"transliterate":{"in":[],"out":[]},"variableRegionLength":40,"countTableFile":"jobs/c9b263b23beb/countTable.7.tsv.gz","modeledColumns":[0,1],"inputFileType":"tsv.gz","nColumns":2,"rightFlank":"TGGAATTCTCGGGTGTCAAGG","componentName":"Count table 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±
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Dinucleotide (10bp)
