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": "GAGTTCTACAGTCCGACCTGG", "nColumns": 3, "modeledColumns": [0, 1, 2], "countTableFile": "jobs/63651f03515e/countTable.0.tsv.gz", "rightFlank": "CCAGGACTCGGACCTGGA", "inputFileType": "tsv.gz", "variableRegionLength": 10}, {"function": "addSELEX", "concentration": 100, "cumulativeEnrichment": false, "modelType": "RhoGamma"}, {"function": "addNS"}, {"function": "addBindingMode", "flankLength": 6, "dinucleotideDistance": 10, "size": 10}, {"function": "bindingModeConstraints", "index": 0, "roundSpecificActivity": false}, {"function": "bindingModeConstraints", "index": 1, "roundSpecificActivity": false}, {"function": "enrichmentModelSeed", "index": 0, "gamma": [0, -1, -1], "rho": [0, 1, 0]}, {"function": "bindingModeSeed", "index": 1, "mononucleotideString": "..TAATTG.."}, {"function": "output", "outputPath": "jobs/63651f03515e", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]Configuration File
±
ProBound configuration file:
{
"modelSeeding": {
"enrichmentModel": [{
"rho": [
0,
1,
0
],
"gamma": [
0,
-1,
-1
]
}],
"bindingModes": [
{"seedScale": 1},
{
"seedScale": 1,
"mononucleotideString": "..TAATTG.."
}
]
},
"optimizerSetting": {
"nThreads": 20,
"likelihoodThreshold": 0,
"lambdaL2": 1.0E-6,
"pseudocount": 200,
"patternSearchSettings": {},
"minimizerType": "lbfgs",
"nRetries": 3,
"hkSettings": {},
"output": {
"storeHessian": false,
"outputPath": "jobs/63651f03515e",
"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": false,
"cumulativeEnrichment": false,
"concentration": 100,
"modelType": "RhoGamma",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
}],
"countTable": [{
"leftFlank": "GAGTTCTACAGTCCGACCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 10,
"modeledColumns": [
0,
1,
2
],
"inputFileType": "tsv.gz",
"nColumns": 3,
"rightFlank": "CCAGGACTCGGACCTGGA",
"countTableFile": "jobs/63651f03515e/countTable.0.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": false,
"modifications": []
}
],
"letterComplement": "C-G,A-T"
},
"modelFittingConstraints": {
"enrichmentModel": [{
"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": false,
"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": true,
"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}],"nShifts":0,"countTable":[{}],"addBindingModesSequentially":true,"flankLengths":[0],"bindingModeInteractions":[],"singleModeLengthSweep":false,"bindingModes":[{"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":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":true,"optimizeSize":false}]}
Entry=bindingModes, aEntry=[{"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":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":true,"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}]
> 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: Rho-gamma enrichment model 0
Concentration: 100.0
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 22:05:08.422).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[0,1,2]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 2.7239494749450666
gradient = {0.1667,-0.3322,0.1655}
gradient norm = 0.40686048071027864
Starting Function Value: 2.7239494749450666
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 1.099155428604088 4.999999999999999 12.289225021981062 0.010176167231896
2 5 1.099000965840938 0.030391161817440 0.249691938811434 0.000102732222300
3 6 1.099000950654878 0.000370340285954 1.000000000000000 0.000020720909277
4 7 1.099000950010984 0.000370340285954 1.000000000000000 0.000000001662113
Convergence criteria met.
After: gradient norm = 1.662112852013348E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.0304,4.0586,-2.0282}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-10.6919,-10.6919,-10.6919}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-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): {0.0000,0.0000,0.0000}
> Initial optimization (component0-1-f0).
>> Starting new optimization: component0-1-f0. (2021-05-21 22:05:10.562).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[1,2,3]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0]]},{}]}
Value and gradient before optimization:
=======================================
value = 1.099000950011171
gradient = {-0.0001,-0.0000,0.0000,-0.0000}
gradient norm = 7.225833007035603E-5
Starting Function Value: 1.099000950011171
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 1.099000938271687 0.000308125100986 4.264215636959470 0.000083861233053
2 5 1.099000868089118 0.001332811952559 5.000000000000000 0.000109062645125
3 6 1.098996656973512 0.103380058700173 1.000000000000000 0.001317788333866
4 7 1.098989428413087 0.210011776409221 1.000000000000000 0.002561086638292
5 8 1.098966735689479 0.707813545911378 1.000000000000000 0.004803778375928
6 9 1.098902999483517 2.053140482284071 1.000000000000000 0.007159849363253
7 12 1.098892052480146 0.467812485019711 0.120733340159343 0.007257290002607
8 13 1.098834746552651 0.687225654444065 1.000000000000000 0.004635834273706
9 15 1.098807584882988 0.114505431853582 0.418275083011945 0.000368534927236
10 16 1.098800968824989 0.294374290467001 1.000000000000000 0.002163364140429
11 17 1.098798360796633 0.093221072278345 1.000000000000000 0.002347016715830
12 18 1.098786339685771 0.599395737002016 1.000000000000000 0.003527968226604
13 19 1.098773380816543 0.036031025156989 1.000000000000000 0.000581688139164
14 20 1.098763019770727 0.339832410414201 1.000000000000000 0.000994223069236
15 22 1.098760945183297 0.129789475714077 0.276210159394310 0.001566061831956
16 23 1.098755409026862 0.164422685145153 1.000000000000000 0.001469188810244
17 24 1.098746426622124 0.202094836743795 1.000000000000000 0.000607928819317
18 26 1.098743926392389 0.127256430414649 0.233506080491373 0.001122133593835
19 27 1.098739801440807 0.269156506876749 1.000000000000000 0.002013684738800
20 28 1.098733687251966 0.026362024977214 1.000000000000000 0.000585910611360
21 29 1.098728905702986 0.202517522264655 1.000000000000000 0.001049932445359
22 31 1.098727323170817 0.104516284036118 0.398896360025656 0.001398792810577
23 32 1.098723166473755 0.104383953946074 1.000000000000000 0.000943052398357
24 33 1.098719156228068 0.128244732995579 1.000000000000000 0.000729319564273
25 34 1.098715559559274 0.218441290448935 1.000000000000000 0.001380406060937
26 35 1.098705810413175 0.290801705928531 1.000000000000000 0.000584515437967
27 37 1.098705236450501 0.043353151610706 0.105467033557974 0.000820232364209
28 38 1.098702972958000 0.115459889143255 1.000000000000000 0.000934591703587
29 39 1.098700278394681 0.101484082997707 1.000000000000000 0.000841682721289
30 40 1.098697695564068 0.097435963648412 1.000000000000000 0.000706576902167
31 42 1.098696379454470 0.090643638123768 0.310013239820705 0.000971954689903
32 44 1.098692992829977 0.141480393319570 0.460464255922578 0.000816283121852
33 45 1.098690084733211 0.099009831758571 1.000000000000000 0.000393591169135
34 47 1.098688192762743 0.102983024802338 0.214948204971174 0.000575699380946
35 49 1.098687399898962 0.070718145283311 0.271496640697317 0.000859706122062
36 50 1.098686075256801 0.076899671738596 1.000000000000000 0.000912524659678
37 51 1.098683552597751 0.100212158995279 1.000000000000000 0.000734977097874
38 52 1.098681722455767 0.112250781017133 1.000000000000000 0.000884127960722
39 53 1.098677413090902 0.199635358747698 1.000000000000000 0.000512368004542
40 55 1.098676800981938 0.058823880959787 0.149051074141622 0.000749392674714
41 56 1.098674968662695 0.194919823008994 1.000000000000000 0.001207207927664
42 57 1.098672735488708 0.017871626176414 1.000000000000000 0.000397932115736
43 58 1.098670885192838 0.141030914161670 1.000000000000000 0.000646862354016
44 60 1.098669924866141 0.103120351721142 0.355230863785911 0.000891763314428
45 61 1.098667980573878 0.110354190958293 1.000000000000000 0.000771683786557
46 62 1.098665781531765 0.103709427562696 1.000000000000000 0.000382047350395
47 64 1.098664610292901 0.117333203523054 0.312059772405036 0.000731795670517
48 66 1.098663708814182 0.102814816354660 0.500087764082348 0.000928020266260
49 67 1.098661781361364 0.136414261109782 1.000000000000000 0.000757984320594
50 68 1.098659903795225 0.105208903704691 1.000000000000000 0.000420050774416
51 70 1.098658771132673 0.142122997387345 0.381676755652291 0.000684265065253
52 71 1.098657723889729 0.202748130213950 1.000000000000000 0.001099353923781
53 72 1.098655680339176 0.045208075500028 1.000000000000000 0.000390387360184
54 73 1.098654204348380 0.196493636591651 1.000000000000000 0.000725610041005
55 74 1.098652630763664 0.228018915599247 1.000000000000000 0.000897757069097
56 75 1.098650272439580 0.198205859860601 1.000000000000000 0.000099746780208
57 77 1.098649561630906 0.150671228969551 0.304886642964251 0.000465778650000
58 78 1.098648740932923 0.229045099040244 1.000000000000000 0.000750588671478
59 79 1.098647502642116 0.120854188336610 1.000000000000000 0.000321575198068
60 80 1.098646619270008 0.301304392422383 1.000000000000000 0.000585664854576
61 81 1.098645732455205 0.141704357968413 1.000000000000000 0.000121072380065
62 82 1.098645445970853 0.310440502284624 1.000000000000000 0.000540887221824
63 83 1.098645130563903 0.013563300484396 1.000000000000000 0.000108356543806
64 84 1.098644979855788 0.133768416948556 1.000000000000000 0.000042042943405
65 85 1.098644925568037 0.137176674723329 1.000000000000000 0.000081973513114
66 86 1.098644914773525 0.015272691575831 1.000000000000000 0.000012299208010
67 87 1.098644914011156 0.015767048002716 1.000000000000000 0.000004774801902
68 88 1.098644913984953 0.001123364396921 1.000000000000000 0.000001178145276
69 89 1.098644913983558 0.001123364396921 1.000000000000000 0.000000114117038
Convergence criteria met.
After: gradient norm = 1.1411703792749282E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.2730,-1.2503,2.5233}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.8315,-0.8315,-0.8315}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-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): {0.0000,0.0000,0.0000}
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 22:05:17.865).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[1,2,3]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0]]},{}]}
Value and gradient before optimization:
=======================================
value = 1.0986449139835583
gradient = {-0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 1.1411703792724233E-7
Already at minimum!
After: gradient norm = 1.1411703792724233E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.2730,-1.2503,2.5233}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.8315,-0.8315,-0.8315}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-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): {0.0000,0.0000,0.0000}
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 22:05:17.958).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[1,2,3]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0]]},{}]}
Value and gradient before optimization:
=======================================
value = 1.0986449139835583
gradient = {-0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 1.141170379278487E-7
Already at minimum!
After: gradient norm = 1.141170379278487E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.2730,-1.2503,2.5233}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.8315,-0.8315,-0.8315}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-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): {0.0000,0.0000,0.0000}
==================================
== Starts fiting Binding mode 1 ==
==================================
> Optimizing h (component1-0-h).
>> Starting new optimization: component1-0-h. (2021-05-21 22:05:19.089).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[0,1,2]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 1.1222116274946359
gradient = {0.0666,0.0713,-0.1378}
gradient norm = 0.1688610555516349
Starting Function Value: 1.1222116274946359
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 1.097532199639091 1.000000000000000 5.922028597613597 0.142394745774837
2 3 1.069613386544253 0.457483803586978 1.000000000000000 0.016996792053017
3 4 1.069171009306119 0.048765474176664 1.000000000000000 0.001094655575766
4 5 1.069169191606847 0.003355943691841 1.000000000000000 0.000011627441632
5 6 1.069169191401920 0.003355943691841 1.000000000000000 0.000000009942682
Convergence criteria met.
After: gradient norm = 9.942681579653037E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.5098,-1.4989,3.0087}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.8315,-0.8315,-0.8315}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-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): {-0.1385,-0.1385,-0.1385}
> Initial optimization (component1-1-f1).
>> Starting new optimization: component1-1-f1. (2021-05-21 22:05:21.167).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[41,42,43]}],"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]]}]}
Value and gradient before optimization:
=======================================
value = 1.0730377747961208
gradient = {-0.0051,0.0020,-0.0062,-0.0014,-0.0048,0.0013,-0.0013,-0.0058,-0.0010,0.0011,0.0037,-0.0145,-0.0139,0.0016,0.0030,-0.0014,-0.0173,0.0031,0.0036,-0.0001,-0.0013,0.0025,0.0022,-0.0141,-0.0012,0.0003,0.0009,-0.0107,-0.0089,0.0013,-0.0009,-0.0021,-0.0043,-0.0039,0.0000,-0.0025,-0.0012,-0.0071,0.0007,-0.0031,-0.0107,-0.0000,0.0000,-0.0000}
gradient norm = 0.03891034925980115
Starting Function Value: 1.0730377747961208
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 1.067444681006476 0.230904182808443 5.934261377781913 0.056954804383184
2 4 1.059941752592730 0.289990148267676 1.000000000000000 0.076992513027598
3 5 1.045653734532363 1.211988851265083 1.000000000000000 0.133603755741452
4 6 1.033798677731100 0.195517775189301 1.000000000000000 0.024873984418074
5 7 1.032639673745454 0.174416841189753 1.000000000000000 0.012004886929478
6 8 1.032191587327903 0.068753696378317 1.000000000000000 0.012910759293769
7 9 1.029194158116035 0.442587756480607 1.000000000000000 0.014546814525119
8 11 1.027714009189474 0.350647948249993 0.435643557039837 0.026262917918536
9 12 1.025138528076600 0.501727864912776 1.000000000000000 0.014481647293472
10 13 1.023872075105982 0.290840970688737 1.000000000000000 0.009332437437358
11 14 1.022747421764986 0.296719711729957 1.000000000000000 0.011153921403253
12 15 1.020791240134878 0.674990371162816 1.000000000000000 0.021712313381733
13 16 1.018997279029553 0.374453358346710 1.000000000000000 0.016293944886126
14 17 1.017168837215682 0.728442456440909 1.000000000000000 0.014095909720151
15 18 1.016358672762857 0.466224078430498 1.000000000000000 0.009064403402353
16 19 1.015525898867212 0.840561529524429 1.000000000000000 0.009066574705284
17 20 1.014954317076976 0.606029989908562 1.000000000000000 0.007472460625672
18 21 1.014750971445790 0.585617588517482 1.000000000000000 0.001740797079171
19 22 1.014696844207115 0.081750520981252 1.000000000000000 0.002287357871434
20 23 1.014617081510860 0.151208071173760 1.000000000000000 0.003006773645607
21 24 1.014505418396456 0.153434615703815 1.000000000000000 0.002402332763935
22 25 1.014359024421037 0.277175578387945 1.000000000000000 0.001046709848437
23 26 1.014324241548659 0.088296709134284 1.000000000000000 0.001225446502251
24 27 1.014289062234246 0.133172964980008 1.000000000000000 0.001235136462085
25 28 1.014251397761643 0.186437379460508 1.000000000000000 0.000967879031947
26 29 1.014232617032736 0.127022499007175 1.000000000000000 0.000229798417398
27 30 1.014229380485792 0.039501913635265 1.000000000000000 0.000343844784023
28 31 1.014227506809351 0.021047766253068 1.000000000000000 0.000359360997720
29 32 1.014223356254981 0.052788041406150 1.000000000000000 0.000181032351619
30 33 1.014221545243233 0.035092008028935 1.000000000000000 0.000107254133605
31 34 1.014220313280479 0.028322607458422 1.000000000000000 0.000139874974317
32 35 1.014218883553442 0.039853869684572 1.000000000000000 0.000184029944489
33 36 1.014216940423520 0.055748532094268 1.000000000000000 0.000170528739593
34 37 1.014214603398069 0.087302060944236 1.000000000000000 0.000138058638116
35 38 1.014213814870945 0.060899287793438 1.000000000000000 0.000139497331714
36 39 1.014213269560649 0.013442559911546 1.000000000000000 0.000069117652473
37 40 1.014212805835604 0.016460150769780 1.000000000000000 0.000061001739686
38 41 1.014212136615604 0.036791869415468 1.000000000000000 0.000069367431935
39 42 1.014211543516935 0.049936975550944 1.000000000000000 0.000050434900521
40 43 1.014211221648475 0.036777064373704 1.000000000000000 0.000035837421121
41 44 1.014211022078679 0.024449766733675 1.000000000000000 0.000042392873489
42 45 1.014210879870569 0.016482827453392 1.000000000000000 0.000051262357104
43 46 1.014210691432211 0.023719739430182 1.000000000000000 0.000049684248557
44 47 1.014210641598768 0.032045624002597 1.000000000000000 0.000078296743360
45 48 1.014210525917610 0.007999745674086 1.000000000000000 0.000018276921449
46 49 1.014210506315860 0.003256604911311 1.000000000000000 0.000011923167226
47 50 1.014210487748586 0.004074870025398 1.000000000000000 0.000016704358909
48 51 1.014210455444544 0.008246775680726 1.000000000000000 0.000024010881974
49 52 1.014210409564980 0.012657082443785 1.000000000000000 0.000024800094746
50 53 1.014210324586248 0.024184746478128 1.000000000000000 0.000026088027200
51 54 1.014210232315936 0.036576254373474 1.000000000000000 0.000023176252784
52 55 1.014210153743308 0.019235877847080 1.000000000000000 0.000022371924870
53 56 1.014209920637956 0.066653512746912 1.000000000000000 0.000048947141119
54 57 1.014209632426379 0.098104855889419 1.000000000000000 0.000070994531311
55 58 1.014209189108893 0.172624194176921 1.000000000000000 0.000084326167111
56 59 1.014208718979627 0.193022522984182 1.000000000000000 0.000063216304498
57 60 1.014208369142895 0.169927641861050 1.000000000000000 0.000023710350647
58 61 1.014208209178531 0.038723294831739 1.000000000000000 0.000047988952906
59 62 1.014207974814364 0.046462809278263 1.000000000000000 0.000093011409960
60 63 1.014207623655837 0.087542553540412 1.000000000000000 0.000129504512089
61 64 1.014206859523773 0.251118778471361 1.000000000000000 0.000162301510371
62 65 1.014205945424815 0.399793599896771 1.000000000000000 0.000149046874589
63 67 1.014205716237282 0.167599976898810 0.458128038611655 0.000073836830690
64 68 1.014205423264584 0.116166334126889 1.000000000000000 0.000043451940437
65 69 1.014205343971765 0.038459578756211 1.000000000000000 0.000014554424809
66 70 1.014205340909302 0.009800266004535 1.000000000000000 0.000004999115090
67 71 1.014205339344920 0.008511423547004 1.000000000000000 0.000006241816832
68 72 1.014205338423433 0.001881461458398 1.000000000000000 0.000010676644289
69 73 1.014205336298668 0.002092968771219 1.000000000000000 0.000018264146526
70 74 1.014205333915109 0.005023171897446 1.000000000000000 0.000021447461469
71 75 1.014205328460647 0.008121408208464 1.000000000000000 0.000022430859421
72 76 1.014205307328429 0.018751874942438 1.000000000000000 0.000033390494646
73 77 1.014205270407175 0.034371147157149 1.000000000000000 0.000036315697839
74 78 1.014205243967258 0.049327052731046 1.000000000000000 0.000032408462833
75 79 1.014205203474949 0.012843207577906 1.000000000000000 0.000021859670693
76 80 1.014205179229464 0.010978252174270 1.000000000000000 0.000006039536186
77 81 1.014205170096779 0.006776471294296 1.000000000000000 0.000013239864161
78 82 1.014205159550961 0.007736077876078 1.000000000000000 0.000022133932803
79 83 1.014205131669303 0.021395528206342 1.000000000000000 0.000037459680517
80 84 1.014205068999242 0.052687056319656 1.000000000000000 0.000058006204083
81 85 1.014204936853437 0.122781584242099 1.000000000000000 0.000080225935877
82 86 1.014204734593400 0.210884291669142 1.000000000000000 0.000085892292599
83 87 1.014204702064334 0.235406768893715 1.000000000000000 0.000058719645100
84 88 1.014204528977103 0.021569922331051 1.000000000000000 0.000039414124091
85 89 1.014204497289931 0.016447092713375 1.000000000000000 0.000013365593629
86 90 1.014204493034828 0.005915856598576 1.000000000000000 0.000001481827489
87 91 1.014204492881176 0.000458563936453 1.000000000000000 0.000001213731425
88 92 1.014204492821258 0.000458563936453 1.000000000000000 0.000000650730127
Convergence criteria met.
After: gradient norm = 6.507301267687958E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.5190,-1.5083,3.0273}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.8315,-0.8315,-0.8315}
Binding mode 1:
---------------
Mononucleotide: {-1.0196,-1.1181,-0.7542,-0.8140,-0.7389,-1.1094,-1.3357,-0.5220,-0.8828,-1.7690,-2.5881,1.5339,2.2144,-2.8187,-0.4120,-2.6898,3.0225,-2.3209,-2.1965,-2.2112,-1.4619,-1.8213,-1.6621,1.2391,-1.3693,-1.2645,-1.2330,0.1607,0.0192,-2.2053,0.1386,-1.6586,-1.2442,-0.6749,-0.7386,-1.0482,-1.1904,-0.6433,-1.3306,-0.5416}
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): {-1.2352,-1.2352,-1.2352}
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 22:06:12.986).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[41,42,43]}],"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]]}]}
Value and gradient before optimization:
=======================================
value = 1.014204492821258
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}
gradient norm = 6.507301267684823E-7
Already at minimum!
After: gradient norm = 6.507301267684823E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.5190,-1.5083,3.0273}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.8315,-0.8315,-0.8315}
Binding mode 1:
---------------
Mononucleotide: {-1.0196,-1.1181,-0.7542,-0.8140,-0.7389,-1.1094,-1.3357,-0.5220,-0.8828,-1.7690,-2.5881,1.5339,2.2144,-2.8187,-0.4120,-2.6898,3.0225,-2.3209,-2.1965,-2.2112,-1.4619,-1.8213,-1.6621,1.2391,-1.3693,-1.2645,-1.2330,0.1607,0.0192,-2.2053,0.1386,-1.6586,-1.2442,-0.6749,-0.7386,-1.0482,-1.1904,-0.6433,-1.3306,-0.5416}
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): {-1.2352,-1.2352,-1.2352}
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 22:06:13.541).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[761,762,763]}],"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]],"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 = 1.1472887514887733
gradient = 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gradient norm = 0.004194695728393202
Starting Function Value: 1.1472887514887733
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 1.146640526354869 0.300603911677348 71.662864517826730 0.022770080146013
2 4 1.145663021532107 0.306267469086826 1.000000000000000 0.014709724748633
3 5 1.144506617549442 0.579983216998212 1.000000000000000 0.007655970313851
4 6 1.143925614270824 0.447213208185998 1.000000000000000 0.004243024352762
5 7 1.143604209585894 0.346698964159625 1.000000000000000 0.003294862299540
6 8 1.143391638767483 0.171012625901704 1.000000000000000 0.003701362909630
7 9 1.143246032807911 0.156371118076695 1.000000000000000 0.006153470598500
8 10 1.143079363652397 0.138036796451548 1.000000000000000 0.003803759738386
9 11 1.142928346913540 0.113469392506188 1.000000000000000 0.003371142640191
10 12 1.142679092873351 0.241627843419281 1.000000000000000 0.003559281770611
11 13 1.142445947019988 0.268348339970192 1.000000000000000 0.002827633550855
12 14 1.142234458773781 0.373981459628319 1.000000000000000 0.002175446355517
13 15 1.142109495588914 0.253634716326582 1.000000000000000 0.001607996858211
14 16 1.142038911580515 0.164811313598092 1.000000000000000 0.001535754867160
15 17 1.141925367906071 0.290802723977832 1.000000000000000 0.001347022055824
16 19 1.141872246756289 0.199614123694416 0.486714914133504 0.001955920518918
17 20 1.141807355594691 0.158958594347679 1.000000000000000 0.001077468581155
18 21 1.141758899667848 0.137400740595018 1.000000000000000 0.000961286567592
19 22 1.141706640557337 0.143836175467355 1.000000000000000 0.001117768423374
20 23 1.141619980419338 0.312747772955887 1.000000000000000 0.001101157007673
21 24 1.141556666653455 0.313262982709534 1.000000000000000 0.001411713895457
22 25 1.141512392453920 0.205375941638852 1.000000000000000 0.000851560373484
23 26 1.141473526281080 0.183384452112842 1.000000000000000 0.000894882881611
24 27 1.141410984030246 0.277284580704033 1.000000000000000 0.001057840767894
25 28 1.141280707844192 0.742065883914612 1.000000000000000 0.001360235658604
26 29 1.141238831167849 0.894758017114656 1.000000000000000 0.002778448106436
27 30 1.141136265126681 0.187162085436456 1.000000000000000 0.000920921551618
28 31 1.141084008657743 0.124097159848402 1.000000000000000 0.000965898081648
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205 215 1.140447038426728 0.004096162732851 1.000000000000000 0.000007914873944
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207 217 1.140447024986704 0.003559528996646 1.000000000000000 0.000007927440824
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209 219 1.140447017334852 0.006447222219451 1.000000000000000 0.000015252719560
210 220 1.140447016707143 0.015183447602278 1.000000000000000 0.000050420738976
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237 247 1.140446964909579 0.001860423984678 1.000000000000000 0.000004357192130
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239 250 1.140446963681371 0.002978240808649 0.357597618308655 0.000003275577149
240 251 1.140446963283217 0.001389106362146 1.000000000000000 0.000003541666866
241 252 1.140446962877433 0.002506052291746 1.000000000000000 0.000003781297435
242 253 1.140446962234669 0.003995787313956 1.000000000000000 0.000002888004972
243 254 1.140446961782796 0.005235740533127 1.000000000000000 0.000003803691076
244 255 1.140446961462482 0.001570358776824 1.000000000000000 0.000002209431906
245 256 1.140446961320076 0.000807406640975 1.000000000000000 0.000002073579036
246 257 1.140446961101499 0.001216019408160 1.000000000000000 0.000001950600325
247 259 1.140446960959401 0.000918494794998 0.401734121358812 0.000002947231229
248 260 1.140446960751346 0.000652286772356 1.000000000000000 0.000002259291119
249 261 1.140446960515267 0.000948515076292 1.000000000000000 0.000002081389444
250 262 1.140446960399140 0.000429732581475 1.000000000000000 0.000001584588854
251 263 1.140446960270330 0.000614729513079 1.000000000000000 0.000001662137452
252 265 1.140446960207769 0.000346604406139 0.383481370886442 0.000001621842900
253 266 1.140446960148668 0.000249814337338 1.000000000000000 0.000001544606144
254 267 1.140446960041762 0.000406581425327 1.000000000000000 0.000001446052351
255 268 1.140446959950925 0.000556884706170 1.000000000000000 0.000001139939137
256 269 1.140446959865033 0.001051852484414 1.000000000000000 0.000001015565637
257 270 1.140446959819496 0.000414751838403 1.000000000000000 0.000000946298381
258 271 1.140446959789208 0.000170252405602 1.000000000000000 0.000000973929320
259 272 1.140446959751169 0.000261103712351 1.000000000000000 0.000000851757774
260 273 1.140446959720149 0.000303561606478 1.000000000000000 0.000000762018102
261 274 1.140446959686088 0.000507729270709 1.000000000000000 0.000000704778102
262 275 1.140446959653071 0.000507729270709 1.000000000000000 0.000000654027136
Convergence criteria met.
After: gradient norm = 6.540271361527352E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.5203,-1.5097,3.0299}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.8315,-0.8315,-0.8315}
Binding mode 1:
---------------
Mononucleotide: {-0.3854,-0.3944,-0.4116,-0.3607,-0.3397,-0.4567,-0.4843,-0.2714,-0.3035,-0.5864,-0.6868,0.0246,0.2271,-0.7735,-0.3331,-0.6726,0.3757,-0.6669,-0.6502,-0.6107,-0.5057,-0.5008,-0.6102,0.0646,-0.4668,-0.4338,-0.5292,-0.1222,-0.1537,-0.6988,-0.1602,-0.5393,-0.4571,-0.3631,-0.3523,-0.3795,-0.4531,-0.3537,-0.4879,-0.2574}
Dinucleotide(d=1): {-0.1734,0.0546,-0.1760,-0.0792,-0.1999,-0.1305,0.0638,-0.1179,0.1150,-0.1218,-0.1928,-0.2178,-0.0858,-0.2559,-0.1731,0.1397,-0.2277,0.0067,-0.3696,0.2003,0.1122,-0.2701,-0.2633,-0.0427,-0.2618,-0.1789,0.0307,-0.0540,0.0311,-0.1368,-0.0854,-0.0415,-0.1227,-0.1561,0.1025,-0.0633,-0.1629,-0.0746,-0.1531,-0.0961,-0.3203,-0.0783,-0.0887,-0.0972,0.6680,-0.3786,-0.1764,-0.3532,0.8281,-0.3589,-0.2575,-0.3067,-0.5074,-0.0494,-0.0515,-0.0489,0.1259,-0.1032,-0.1635,-0.1041,-0.3932,-0.0507,-0.0600,-0.0500,-0.1039,-0.0823,-0.1935,0.6636,-0.1183,-0.1352,-0.1019,-0.2735,-0.1039,-0.1121,-0.1020,-0.3030,-0.1044,-0.0970,-0.1253,-0.2584,-0.6427,0.6776,-0.5145,-0.2111,0.4911,-0.5933,0.2211,-0.7524,-0.4019,-0.3256,-0.4971,0.5945,0.1171,-0.2951,0.3657,0.2158,-0.3251,0.1989,-0.1711,-0.0656,-0.3050,-0.6302,0.1577,0.2742,0.2950,0.0067,-0.5806,-0.2700,0.2017,-0.2552,0.3701,-0.4525,-0.8169,0.4138,-0.2052,0.2027,0.1120,-0.4329,-0.1465,-0.1441,0.0156,-0.0751,0.0515,-0.0211,0.1250,-0.3477,0.0668,-0.3487,-0.4323,-0.0606,0.0091,-0.0066,0.0262,-0.1529,-0.2507,0.0130,-0.0727,-0.1040,-0.0473,-0.1047,-0.0119,-0.0195,-0.1959,-0.1400}
Dinucleotide(d=2): {-0.2349,-0.0667,-0.2243,0.1230,-0.0421,-0.1132,-0.1054,-0.1108,-0.0618,-0.1023,-0.2655,0.0221,0.0071,-0.3154,-0.0781,0.0173,-0.0688,-0.1552,0.0789,-0.1790,0.1536,-0.1610,-0.3172,-0.1536,0.0171,-0.2033,-0.1703,-0.1034,0.1783,-0.2225,-0.0095,-0.2352,0.0735,-0.0946,-0.1077,-0.0812,-0.2290,-0.0830,-0.0782,-0.0809,-0.3585,-0.0866,-0.0539,-0.0750,0.7249,-0.3404,-0.3572,-0.3231,0.0365,0.0670,-0.0508,0.2616,-0.1096,-0.1225,-0.1161,-0.3763,-0.3225,-0.3013,-0.2441,0.3628,-0.0912,-0.1269,-0.1432,-0.2744,0.0062,0.0214,-0.0487,0.4357,-0.1978,-0.1112,-0.1380,-0.2270,-0.1460,-0.1674,-0.1629,-0.1811,-0.0960,-0.1445,-0.1335,-0.2600,-0.3040,-0.1142,0.0311,-0.0539,0.3867,-0.0775,-0.6183,-0.3798,-0.2592,-0.3601,0.2549,-0.2584,-0.0194,-0.0421,0.0909,0.1722,-0.2513,-0.0209,-0.0107,-0.1826,-0.0336,-0.1441,-0.3894,0.0939,-0.2203,-0.1924,-0.0028,-0.1008,0.0495,0.0114,0.0284,-0.1852,-0.0735,0.0117,0.0825,-0.1770,-0.1851,-0.1139,-0.3426,-0.0426,-0.1656,-0.0729,-0.0744,0.1414,-0.0147,-0.1643,-0.1736,-0.1864}
Dinucleotide(d=3): {0.0025,-0.1544,-0.0221,-0.1991,0.0345,-0.1393,-0.1706,-0.1050,0.1615,-0.2752,-0.1111,-0.2167,0.0823,-0.1890,-0.0878,-0.1616,0.1428,-0.1756,-0.1377,-0.1722,0.0796,-0.1614,-0.2473,-0.1222,0.0127,-0.1637,-0.1485,-0.1599,0.2270,-0.1874,-0.1455,-0.1918,-0.1468,-0.0683,-0.1297,0.0483,-0.1972,-0.1015,-0.1166,-0.1360,-0.1951,-0.0555,-0.0868,-0.3124,0.0417,-0.2612,-0.2412,0.4073,-0.0040,0.1116,0.0613,0.1249,-0.1556,-0.1413,-0.2186,-0.2291,-0.1900,-0.2565,-0.1472,0.1653,-0.0991,-0.1586,-0.2177,-0.1965,0.3772,-0.3383,0.4363,-0.1582,-0.1900,-0.0924,-0.2562,-0.1033,-0.2217,-0.1076,-0.1759,-0.1193,-0.1692,-0.0790,-0.2678,-0.0853,-0.0635,-0.0373,-0.0636,-0.3469,-0.4431,0.0246,-0.2648,0.1121,-0.2022,-0.2982,0.0009,-0.0959,0.2000,-0.0293,0.0049,-0.0486,-0.1437,-0.0748,-0.0132,-0.2268,-0.1780,-0.1133,-0.4063,0.1926,-0.1235,-0.1109,-0.0908,-0.1802,0.0098,-0.0303,0.0024,-0.0641}
Dinucleotide(d=4): {0.0630,-0.1418,-0.1296,-0.1581,0.0971,-0.1575,-0.2092,-0.1172,0.2105,-0.2402,-0.2041,-0.2152,0.0966,-0.1522,-0.1356,-0.1574,-0.1244,-0.1721,-0.0632,0.0240,-0.2112,-0.0827,-0.2408,0.0647,-0.1648,-0.1496,-0.2323,0.0564,-0.0254,-0.1101,-0.0828,-0.0367,-0.0946,-0.0558,-0.1180,-0.0565,-0.1806,-0.1609,-0.2731,0.0072,-0.1468,-0.2225,-0.1983,-0.1053,-0.0425,-0.0029,0.0457,0.0540,0.2212,-0.0290,0.2169,-0.1252,-0.2574,-0.1066,-0.2566,-0.1030,0.1062,-0.3973,0.1246,-0.2803,-0.2561,-0.1227,-0.2864,0.0008,-0.0356,0.2561,0.1988,0.0327,-0.1133,-0.2355,-0.2093,-0.1298,-0.1270,-0.2315,-0.1843,-0.1306,-0.1426,-0.2022,-0.1756,-0.1211,-0.1242,-0.1301,-0.1850,-0.0781,-0.2664,0.0034,-0.2003,-0.0687,-0.1754,-0.1567,-0.1892,-0.0860,0.0946,-0.0620,0.0781,-0.0051}
Dinucleotide(d=5): {-0.0395,-0.2239,-0.1148,-0.0054,-0.2111,-0.1043,-0.1249,0.0446,-0.1231,-0.1590,-0.1887,0.0567,-0.1522,-0.0361,-0.1817,0.0125,-0.0958,-0.0885,-0.0708,-0.0811,-0.1861,-0.1398,-0.1567,0.0179,-0.1203,-0.1350,-0.1793,-0.0477,-0.0712,-0.0768,-0.1233,0.0036,0.1197,-0.3494,0.0461,-0.1959,-0.1568,-0.1445,-0.0766,-0.2020,-0.1201,-0.1827,-0.1625,-0.1939,-0.0016,-0.0097,0.0356,0.0433,0.0236,0.1028,0.1342,0.0202,-0.1724,-0.2571,-0.1782,-0.1500,-0.1345,-0.0949,-0.0774,-0.0822,-0.1608,-0.1225,-0.2481,-0.1537,0.0010,0.2791,-0.0499,0.2142,-0.1522,-0.2608,-0.1077,-0.1654,-0.1271,-0.2133,-0.1547,-0.1743,-0.1413,-0.2223,-0.1353,-0.1409}
Dinucleotide(d=6): {-0.1004,-0.1094,-0.1351,-0.0380,-0.1437,-0.1553,-0.1233,0.0225,-0.1341,-0.0732,-0.1719,-0.0329,-0.0940,-0.1038,-0.0993,-0.0590,-0.0449,-0.1161,-0.0351,-0.1401,-0.0245,-0.2726,-0.0192,-0.1528,-0.0573,-0.2227,-0.0452,-0.1594,-0.0277,-0.0770,-0.0625,-0.0941,-0.1228,-0.1178,-0.0289,-0.0608,-0.1252,-0.1314,-0.1977,-0.1384,-0.1452,-0.1276,-0.2382,-0.1650,-0.0520,0.0187,0.0914,-0.0100,0.0174,0.1493,0.0189,0.0969,-0.1442,-0.2938,-0.1302,-0.1914,-0.1418,-0.0245,-0.1715,-0.0543,-0.1704,-0.2195,-0.1913,-0.1004}
Dinucleotide(d=7): {-0.0440,-0.1787,-0.0314,-0.1286,0.0227,-0.2607,-0.0204,-0.1501,-0.0559,-0.1310,-0.1061,-0.1100,-0.0800,-0.1125,-0.0068,-0.1573,-0.0926,-0.1100,-0.0665,-0.0718,-0.1326,-0.1281,-0.0858,-0.1106,-0.1194,-0.0922,-0.1491,-0.1225,-0.1100,-0.0337,-0.0518,-0.0743,-0.1149,-0.0724,-0.1437,-0.0017,-0.1836,-0.1367,-0.1331,-0.1384,-0.1892,-0.1342,-0.2548,-0.1010,0.0302,-0.0060,0.0359,-0.0073}
Dinucleotide(d=8): {-0.1108,-0.1249,-0.0649,-0.0841,-0.0757,-0.0973,-0.1397,-0.0812,-0.1711,-0.0560,-0.0803,-0.1057,-0.0992,-0.0848,-0.0676,-0.1076,-0.0860,-0.0339,-0.1076,-0.1122,-0.0911,-0.1736,-0.1758,-0.0214,-0.1739,-0.1134,-0.1233,-0.0717,-0.1022,-0.0381,-0.0791,-0.0475}
Dinucleotide(d=9): {-0.0722,-0.0831,-0.1415,-0.0840,-0.0658,-0.1410,-0.1929,0.0007,-0.1258,-0.0628,-0.0608,-0.1594,-0.1903,-0.0660,-0.0917,-0.0143}
Activity(exp=0): {-0.5171,-0.5171,-0.5171}
> Optimizing the full model (component1-4-all).
>> Starting new optimization: component1-4-all. (2021-05-21 22:15:38.75).
>>> Packing before optimization
Packing: {"enrichmentModel":[{}],"countTable":[{"h":[762,763,764]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0]]},{"mononucleotide":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40],"activity":[[761,761,761]],"dinucleotide":[[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],[745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760]]}]}
Value and gradient before optimization:
=======================================
value = 1.1404469596530706
gradient = 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gradient norm = 0.002031824340107683
Starting Function Value: 1.1404469596530706
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
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209 226 0.941143486344317 0.003388691431744 1.000000000000000 0.000008988909423
210 227 0.941143480449382 0.004202747474155 1.000000000000000 0.000010576387904
211 228 0.941143472296951 0.006735044238878 1.000000000000000 0.000012329344341
212 229 0.941143461229902 0.012443539390442 1.000000000000000 0.000016567690004
213 230 0.941143457383232 0.015956173633167 1.000000000000000 0.000020114948911
214 231 0.941143448732306 0.004011234481914 1.000000000000000 0.000006884783626
215 232 0.941143445737203 0.001137565201598 1.000000000000000 0.000008584403941
216 234 0.941143444132081 0.001479399239054 0.459094862415713 0.000014336945206
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226 245 0.941143420661894 0.001736564653805 1.000000000000000 0.000008499230130
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237 257 0.941143406108421 0.000485760804465 1.000000000000000 0.000003514543714
238 258 0.941143405617590 0.000635787829336 1.000000000000000 0.000003999168790
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240 261 0.941143404383781 0.000711459634910 0.239326657801623 0.000005828607231
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242 263 0.941143403446981 0.000724053283084 1.000000000000000 0.000002907517182
243 264 0.941143403112561 0.000820257376975 1.000000000000000 0.000006818101262
244 265 0.941143402775267 0.000326034909191 1.000000000000000 0.000003502724645
245 266 0.941143402501262 0.000297427275113 1.000000000000000 0.000003033574845
246 267 0.941143402151957 0.000684834912707 1.000000000000000 0.000006271806689
247 268 0.941143401920504 0.000620830261128 1.000000000000000 0.000004046962384
248 269 0.941143401685903 0.000854221098514 1.000000000000000 0.000004009127552
249 270 0.941143401467352 0.000953719973762 1.000000000000000 0.000002593197509
250 271 0.941143401302962 0.000422458509249 1.000000000000000 0.000002712083385
251 272 0.941143401002638 0.000658232870792 1.000000000000000 0.000005575031729
252 273 0.941143400759525 0.000657650322383 1.000000000000000 0.000003308639294
253 274 0.941143400579677 0.000384709185672 1.000000000000000 0.000004177262600
254 275 0.941143400432025 0.000290076909843 1.000000000000000 0.000002545828520
255 276 0.941143400272687 0.000369545511522 1.000000000000000 0.000002799217731
256 277 0.941143400133813 0.000402677014154 1.000000000000000 0.000003963642555
257 278 0.941143399924224 0.000612927192065 1.000000000000000 0.000004217125757
258 279 0.941143399581082 0.000916622635497 1.000000000000000 0.000002765349348
259 281 0.941143399427971 0.000555346806122 0.406838732778462 0.000004944209124
260 282 0.941143399246512 0.000442248666319 1.000000000000000 0.000001547219835
261 283 0.941143399183807 0.000113809257671 1.000000000000000 0.000002062007882
262 284 0.941143399100287 0.000149211968122 1.000000000000000 0.000002506453880
263 285 0.941143398910743 0.000483627008440 1.000000000000000 0.000002427673083
264 287 0.941143398841339 0.000337274803324 0.249907414616279 0.000004753078863
265 288 0.941143398664354 0.000704201425101 1.000000000000000 0.000001906909188
266 289 0.941143398590062 0.000704201425101 1.000000000000000 0.000001368963159
Convergence criteria met.
After: gradient norm = 1.3689631593207231E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.9796,1.9014,-0.9218}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-11.0721,-11.0721,-11.0721}
Binding mode 1:
---------------
Mononucleotide: {-0.7464,-0.7353,-0.7245,-0.7055,-0.6637,-0.8471,-0.7948,-0.6060,-0.6272,-0.9766,-0.9883,-0.3196,-0.0511,-1.2036,-0.6429,-1.0140,0.1484,-1.0306,-0.9802,-1.0492,-0.8934,-0.8080,-0.9908,-0.2195,-0.8511,-0.7446,-0.8941,-0.4219,-0.4738,-1.0815,-0.4761,-0.8802,-0.8359,-0.6912,-0.6970,-0.6875,-0.8200,-0.6866,-0.8470,-0.5581}
Dinucleotide(d=1): {-0.2817,0.0098,-0.3110,-0.1563,-0.2654,-0.2765,0.0271,-0.2123,0.0605,-0.2014,-0.2904,-0.2971,-0.1794,-0.3798,-0.2209,0.0636,-0.3307,-0.0217,-0.5289,0.1480,0.0603,-0.3861,-0.3904,-0.1340,-0.3544,-0.2775,0.0382,-0.1808,-0.0364,-0.2705,-0.1412,-0.1049,-0.1951,-0.2889,0.0132,-0.0799,-0.2177,-0.1626,-0.2251,-0.2439,-0.4429,-0.1507,-0.1045,-0.1905,0.6225,-0.4884,-0.3158,-0.4408,0.8065,-0.4895,-0.2930,-0.4463,-0.7105,-0.1209,-0.1248,-0.1203,0.1125,-0.1808,-0.2835,-0.2008,-0.4384,-0.1260,-0.1459,-0.1496,-0.1453,-0.1165,-0.3377,0.6434,-0.2101,-0.1863,-0.1462,-0.4643,-0.2160,-0.2348,-0.1809,-0.3160,-0.2276,-0.1878,-0.2228,-0.3622,-0.9538,0.6967,-0.6259,-0.2798,0.5104,-0.7558,0.1792,-0.8790,-0.5577,-0.3461,-0.7312,0.6113,0.1066,-0.4363,0.3948,0.1554,-0.4321,0.1465,-0.2242,-0.1999,-0.4555,-0.7835,0.0782,0.2972,0.2607,-0.0636,-0.7047,-0.4060,0.1676,-0.3469,0.3277,-0.5726,-1.0580,0.3831,-0.3071,0.1658,0.0571,-0.5828,-0.1929,-0.2503,-0.0638,-0.1243,-0.0477,-0.0630,0.0710,-0.4627,0.0127,-0.4483,-0.6169,-0.1238,-0.0612,-0.0860,-0.0330,-0.2326,-0.3916,-0.0393,-0.1551,-0.2010,-0.1043,-0.2027,-0.0765,-0.1024,-0.2870,-0.1978}
Dinucleotide(d=2): {-0.3200,-0.1455,-0.3802,0.0704,-0.1379,-0.2353,-0.1199,-0.2147,-0.1461,-0.1652,-0.3438,-0.0578,-0.0465,-0.4323,-0.1453,-0.0910,-0.2089,-0.2433,-0.0092,-0.1672,0.1200,-0.2100,-0.3468,-0.4488,-0.0484,-0.3408,-0.2691,-0.1118,0.1357,-0.3528,-0.0966,-0.3131,-0.0763,-0.1041,-0.1385,-0.1239,-0.2716,-0.1639,-0.1901,-0.1437,-0.5348,-0.1440,-0.0203,-0.1437,0.7911,-0.5257,-0.5793,-0.5423,-0.0407,0.0282,-0.0677,0.1312,-0.2349,-0.2060,-0.2327,-0.4599,-0.4342,-0.3708,-0.3295,0.2921,-0.1733,-0.2634,-0.3165,-0.2333,-0.0353,0.0212,-0.1131,0.3489,-0.3110,-0.1781,-0.2586,-0.2979,-0.3027,-0.3252,-0.2499,-0.1361,-0.1707,-0.2460,-0.2181,-0.4387,-0.3836,-0.2288,-0.0200,-0.1644,0.3285,-0.0784,-0.7737,-0.5083,-0.3529,-0.6237,0.2400,-0.3084,-0.0855,-0.0634,-0.0225,0.1340,-0.4245,-0.0836,-0.0582,-0.2938,-0.1099,-0.2258,-0.5067,0.0487,-0.3471,-0.2725,-0.0849,-0.1692,0.0291,-0.0796,-0.0678,-0.2653,-0.1884,-0.0635,0.0351,-0.2651,-0.2898,-0.2169,-0.4586,-0.0988,-0.2369,-0.1498,-0.1610,0.0638,-0.0869,-0.2398,-0.2954,-0.2589}
Dinucleotide(d=3): {-0.0378,-0.2270,-0.0863,-0.3976,-0.0615,-0.2220,-0.2401,-0.1865,0.0726,-0.4030,-0.2104,-0.2054,0.0377,-0.3174,-0.1761,-0.2502,0.0788,-0.2232,-0.1979,-0.3134,0.0916,-0.3088,-0.4490,-0.2045,-0.0806,-0.1916,-0.2395,-0.2399,0.1675,-0.3354,-0.1532,-0.3120,-0.2509,-0.1827,-0.1820,0.0053,-0.3153,-0.1544,-0.2647,-0.1879,-0.3014,-0.0659,-0.1530,-0.4428,-0.0152,-0.4042,-0.3445,0.3485,-0.0707,0.0118,0.0416,0.0401,-0.2624,-0.2776,-0.3438,-0.2670,-0.2630,-0.3574,-0.1863,0.0621,-0.2331,-0.1328,-0.4298,-0.2429,0.3083,-0.4684,0.4046,-0.1477,-0.2646,-0.1387,-0.4404,-0.1786,-0.2733,-0.2132,-0.2115,-0.2650,-0.2830,-0.1676,-0.3681,-0.2038,-0.1831,-0.1372,-0.1063,-0.4674,-0.5745,-0.0439,-0.3648,0.0766,-0.3420,-0.3564,-0.0797,-0.1838,0.1839,-0.1117,-0.1038,-0.1172,-0.2658,-0.1634,-0.0882,-0.3154,-0.2541,-0.2090,-0.5615,0.1730,-0.2197,-0.1859,-0.1674,-0.2867,-0.0540,-0.0942,-0.0601,-0.1586}
Dinucleotide(d=4): {0.0158,-0.2427,-0.2384,-0.2631,0.0811,-0.2709,-0.3216,-0.2300,0.1312,-0.2739,-0.2610,-0.3484,0.0310,-0.2747,-0.2078,-0.2378,-0.2293,-0.2671,-0.1350,-0.0291,-0.3416,-0.1906,-0.3401,0.0082,-0.2246,-0.2236,-0.3454,-0.0098,-0.1185,-0.1490,-0.1787,-0.1369,-0.2032,-0.0835,-0.2346,-0.1219,-0.3203,-0.2672,-0.4275,0.0052,-0.1970,-0.3230,-0.1595,-0.2971,-0.1226,-0.0825,-0.0814,0.0051,0.2153,-0.0384,0.2074,-0.3497,-0.3682,-0.1631,-0.3521,-0.1777,0.1311,-0.5053,0.1376,-0.5693,-0.4953,-0.2615,-0.5142,0.1924,-0.1407,0.2546,0.1876,-0.0753,-0.1902,-0.3361,-0.3270,-0.1994,-0.2163,-0.3715,-0.3172,-0.1201,-0.2254,-0.3197,-0.2755,-0.2389,-0.2173,-0.2265,-0.2665,-0.1908,-0.3605,-0.0797,-0.3088,-0.1047,-0.2933,-0.2404,-0.3083,-0.1458,0.0296,-0.1294,0.0221,-0.0909}
Dinucleotide(d=5): {-0.1392,-0.2805,-0.2223,-0.0960,-0.3282,-0.1834,-0.2232,-0.0084,-0.1976,-0.2478,-0.2645,-0.0159,-0.2512,-0.1265,-0.2779,-0.0484,-0.1767,-0.1561,-0.1521,-0.1736,-0.2912,-0.2172,-0.2895,-0.0575,-0.2190,-0.2305,-0.2470,-0.0991,-0.1703,-0.1515,-0.2073,-0.0724,0.0358,-0.4546,-0.0181,-0.2647,-0.1846,-0.2765,-0.1738,-0.3231,-0.1936,-0.2802,-0.1377,-0.3618,-0.1264,-0.0554,-0.1318,0.0354,0.0070,-0.0290,0.0991,-0.0596,-0.2495,-0.3493,-0.3006,-0.2548,-0.2052,-0.2196,-0.0765,-0.2039,-0.3817,-0.0816,-0.4677,-0.1382,-0.0111,0.2260,-0.0921,0.1193,-0.2770,-0.3210,-0.2190,-0.2406,-0.2241,-0.3168,-0.2768,-0.2045,-0.2836,-0.3507,-0.2172,-0.2218}
Dinucleotide(d=6): {-0.1900,-0.2202,-0.2297,-0.1055,-0.2510,-0.1939,-0.2062,-0.0859,-0.2185,-0.1547,-0.2608,-0.0929,-0.1974,-0.1883,-0.1984,-0.1178,-0.1150,-0.2290,-0.0869,-0.2334,-0.1200,-0.3752,-0.1246,-0.2358,-0.1394,-0.2919,-0.1352,-0.2282,-0.1028,-0.1676,-0.1337,-0.1925,-0.1881,-0.2209,-0.1096,-0.1365,-0.2667,-0.2203,-0.2758,-0.2125,-0.2741,-0.1848,-0.2957,-0.2317,-0.1015,-0.0624,-0.0293,-0.1011,-0.0640,0.0699,-0.0206,0.0257,-0.2384,-0.4137,-0.2246,-0.2935,-0.2573,-0.1120,-0.2532,-0.0957,-0.2416,-0.2654,-0.3432,-0.1836}
Dinucleotide(d=7): {-0.1520,-0.2699,-0.1084,-0.2120,-0.0396,-0.3577,-0.1064,-0.2499,-0.1309,-0.2134,-0.1765,-0.1943,-0.1587,-0.2176,-0.0903,-0.2338,-0.1841,-0.1871,-0.1435,-0.1505,-0.2328,-0.2156,-0.2197,-0.1763,-0.2013,-0.1879,-0.2166,-0.1893,-0.2132,-0.1030,-0.1198,-0.1705,-0.1840,-0.1523,-0.2525,-0.0682,-0.2749,-0.2359,-0.2645,-0.1973,-0.3253,-0.2023,-0.3048,-0.1569,-0.0456,-0.0924,-0.0331,-0.1210}
Dinucleotide(d=8): {-0.2108,-0.2064,-0.1587,-0.1696,-0.1605,-0.1790,-0.2243,-0.1709,-0.2492,-0.1354,-0.1696,-0.1720,-0.2131,-0.1713,-0.1459,-0.1744,-0.1730,-0.1334,-0.1955,-0.1607,-0.2080,-0.2573,-0.2932,-0.0935,-0.2370,-0.1938,-0.2174,-0.1461,-0.2006,-0.1092,-0.1420,-0.1503}
Dinucleotide(d=9): {-0.1717,-0.1752,-0.2212,-0.1727,-0.1650,-0.2100,-0.2898,-0.0759,-0.2004,-0.1339,-0.1604,-0.2260,-0.2839,-0.1687,-0.1750,-0.0814}
Activity(exp=0): {-0.9719,-0.9719,-0.9719}
> Optimization done.
Probound Model
±
Optimized model:
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Mononucleotide (10bp)
Dinucleotide (10bp)
