{
  "modelSeeding": {"bindingModes": [
    {"seedScale": 1},
    {
      "seedScale": 10,
      "mononucleotideString": ".....Y....."
    }
  ]},
  "optimizerSetting": {
    "output": {
      "storeHessian": false,
      "outputPath": "./",
      "printTrajectory": false,
      "baseName": "fit.21937",
      "printPSAM": false,
      "verbose": true
    },
    "nThreads": 20,
    "lbfgsSettings": {
      "memory": 100,
      "convergence": 1.0E-7,
      "MCSearch": true,
      "maxIters": 2000
    },
    "likelihoodThreshold": 0,
    "lambdaL2": 1.0E-6,
    "sgdSettings": {},
    "fixedLibrarySize": false,
    "pseudocount": 5,
    "patternSearchSettings": {},
    "expBound": 40,
    "minimizerType": "lbfgs",
    "nRetries": 3
  },
  "modelSettings": {
    "enrichmentModel": [{
      "r0KUsed": 1,
      "round": 1,
      "bindingSaturation": false,
      "roundSpecificBindingModeInteractions": [[]],
      "concentration": 1,
      "modelType": "SELEX",
      "bindingModeInteractions": [-1],
      "roundSpecificBindingModes": [[]],
      "r0KsTested": [1],
      "bindingModes": [-1],
      "modifications": ["None"]
    }],
    "letterOrder": "ACDEFGHIKLMNPQRSTVWY",
    "countTable": [{
      "leftFlank": "GQSGQ",
      "transliterate": {
        "in": [],
        "out": []
      },
      "variableRegionLength": 11,
      "testFolds": [9],
      "modeledColumns": [
        0,
        1
      ],
      "inputFileType": "tsv.gz",
      "errorModel": "Poisson",
      "nColumns": 2,
      "rightFlank": "GGQSGQSGDY",
      "countTableFile": "../countTables/6624.20230607_nX11_cMyc_cSrc_R1.tsv.gz",
      "probeBias": true
    }],
    "bindingModeInteractions": [],
    "bindingModes": [
      {
        "size": 3,
        "fitLogActivity": true,
        "flankLength": 0,
        "dinucleotideDistance": 0,
        "positionBias": false,
        "singleStrand": true,
        "modifications": []
      },
      {
        "size": 11,
        "fitLogActivity": true,
        "flankLength": 5,
        "dinucleotideDistance": 0,
        "positionBias": false,
        "singleStrand": true,
        "modifications": []
      }
    ],
    "letterComplement": "A-A,C-C,D-D,E-E,F-F,G-G,H-H,I-I,K-K,L-L,M-M,N-N,P-P,Q-Q,R-R,S-S,T-T,V-V,W-W,Y-Y"
  },
  "modelFittingConstraints": {
    "enrichmentModel": [{
      "fitDelta": [false],
      "roundSpecificGamma": true,
      "fitRho": false,
      "roundSpecificDelta": true,
      "fitGamma": false,
      "trySaturation": false,
      "roundSpecificRho": true
    }],
    "nShifts": 0,
    "countTable": [{}],
    "addBindingModesSequentially": true,
    "flankLengths": [0],
    "bindingModeInteractions": [],
    "singleModeLengthSweep": false,
    "bindingModes": [
      {
        "maxFlankLength": -1,
        "positionBiasBinWidth": 1,
        "optimizeSizeHeuristic": false,
        "maxSize": -1,
        "optimizeFlankLength": false,
        "symmetryString": "null",
        "roundSpecificActivity": true,
        "informationThreshold": 0.1,
        "optimizeMotifShift": false,
        "fittingStages": [],
        "optimizeMotifShiftHeuristic": false,
        "experimentSpecificPositionBias": true,
        "minSize": -1,
        "experimentSpecificActivity": true,
        "optimizeSize": false
      },
      {
        "maxFlankLength": -1,
        "positionBiasBinWidth": 1,
        "optimizeSizeHeuristic": false,
        "maxSize": -1,
        "symmetryString": "bcdef.ghijk",
        "optimizeFlankLength": false,
        "roundSpecificActivity": true,
        "informationThreshold": 0.1,
        "optimizeMotifShift": false,
        "fittingStages": [],
        "optimizeMotifShiftHeuristic": false,
        "experimentSpecificPositionBias": true,
        "minSize": -1,
        "experimentSpecificActivity": true,
        "optimizeSize": false
      }
    ]
  }
}