view test-data/relax-out1.json @ 11:beeeed9665ea draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954

{
 "analysis":0,
 "branch attributes":{
   "0":{
     "Baboon":{
       "General descriptive":0.001859058366368826,
       "MG94xREV with separate rates for branch sets":0.001769294089885709,
       "Nucleotide GTR":0.001685167654714891,
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       "RELAX null":0.001859167714920677,
       "RELAX partitioned descriptive":0.001898817195216417,
       "k (general descriptive)":0.09969742933359635,
       "original name":"Baboon"
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     "Cat":{
       "General descriptive":0.3650161006190072,
       "MG94xREV with separate rates for branch sets":0.2796018473093496,
       "Nucleotide GTR":0.2660536011315811,
       "RELAX alternative":0.3685874431614762,
       "RELAX null":0.3167334440346762,
       "RELAX partitioned descriptive":0.3719472357609613,
       "k (general descriptive)":2.319877215422834,
       "original name":"Cat"
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     "Chimp":{
       "General descriptive":0.001895983937468787,
       "MG94xREV with separate rates for branch sets":0.001826027667597702,
       "Nucleotide GTR":0.001820258053351119,
       "RELAX alternative":0.001831530791728368,
       "RELAX null":0.001834052740714585,
       "RELAX partitioned descriptive":0.001832682515795942,
       "k (general descriptive)":5.158328270628251,
       "original name":"Chimp"
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     "Cow":{
       "General descriptive":0.3737128696500712,
       "MG94xREV with separate rates for branch sets":0.2521304147607955,
       "Nucleotide GTR":0.2480198736772598,
       "RELAX alternative":0.3426997068768813,
       "RELAX null":0.2931467439343907,
       "RELAX partitioned descriptive":0.3469082289876269,
       "k (general descriptive)":2.852150041266453,
       "original name":"Cow"
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     "Horse":{
       "General descriptive":0.2804279827409984,
       "MG94xREV with separate rates for branch sets":0.2158535884657318,
       "Nucleotide GTR":0.2090998951755368,
       "RELAX alternative":0.3058441352816696,
       "RELAX null":0.2546949756245578,
       "RELAX partitioned descriptive":0.3035514182923183,
       "k (general descriptive)":1.929916608813313,
       "original name":"Horse"
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     "Human":{
       "General descriptive":0,
       "MG94xREV with separate rates for branch sets":0,
       "Nucleotide GTR":0,
       "RELAX alternative":0,
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       "RELAX partitioned descriptive":0,
       "k (general descriptive)":1.485684693044203,
       "original name":"Human"
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     "Mouse":{
       "General descriptive":0.1308809509233143,
       "MG94xREV with separate rates for branch sets":0.1197584101055861,
       "Nucleotide GTR":0.1181058300538561,
       "RELAX alternative":0.1346294129227689,
       "RELAX null":0.1438267359449897,
       "RELAX partitioned descriptive":0.148454172127534,
       "k (general descriptive)":0.4625550584398252,
       "original name":"Mouse"
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     "Node1":{
       "General descriptive":0.3500691487967139,
       "MG94xREV with separate rates for branch sets":0.2856782993656827,
       "Nucleotide GTR":0.2767105173979571,
       "RELAX alternative":0.385503346940632,
       "RELAX null":0.4352096867868785,
       "RELAX partitioned descriptive":0.4379872513902164,
       "k (general descriptive)":0.4572754180074107
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     "Node12":{
       "General descriptive":0.01767932040676307,
       "MG94xREV with separate rates for branch sets":0.01800350744117403,
       "Nucleotide GTR":0.01784222107494562,
       "RELAX alternative":0.01834159481548459,
       "RELAX null":0.01822563245625142,
       "RELAX partitioned descriptive":0.01881534539472323,
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     "Node2":{
       "General descriptive":0.05767151047612454,
       "MG94xREV with separate rates for branch sets":0.06170856993599769,
       "Nucleotide GTR":0.06614755778044307,
       "RELAX alternative":0.0544792799094392,
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     "Node3":{
       "General descriptive":0.1330088052861041,
       "MG94xREV with separate rates for branch sets":0.09733132151710643,
       "Nucleotide GTR":0.09883748387954429,
       "RELAX alternative":0.1169235247351394,
       "RELAX null":0.1263887172366205,
       "RELAX partitioned descriptive":0.1196402015693241,
       "k (general descriptive)":1.977892771876671
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     "Node8":{
       "General descriptive":0.140412283431793,
       "MG94xREV with separate rates for branch sets":0.1091939823455765,
       "Nucleotide GTR":0.1062201244057951,
       "RELAX alternative":0.1284192265733904,
       "RELAX null":0.1334227466998376,
       "RELAX partitioned descriptive":0.1367904558404228,
       "k (general descriptive)":2.206967022203622
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     "Node9":{
       "General descriptive":0.02664133794298214,
       "MG94xREV with separate rates for branch sets":0.02578742148415842,
       "Nucleotide GTR":0.02567813733543303,
       "RELAX alternative":0.02680940150436639,
       "RELAX null":0.0273694783141817,
       "RELAX partitioned descriptive":0.02747376898615263,
       "k (general descriptive)":0.07343731037788495
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     "Pig":{
       "General descriptive":0.210591346560755,
       "MG94xREV with separate rates for branch sets":0.1903463787974325,
       "Nucleotide GTR":0.1871390433004313,
       "RELAX alternative":0.1974790507889271,
       "RELAX null":0.2130024973755621,
       "RELAX partitioned descriptive":0.2084407457285946,
       "k (general descriptive)":1.581210670484469,
       "original name":"Pig"
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     "Rat":{
       "General descriptive":0.07157977734335202,
       "MG94xREV with separate rates for branch sets":0.06709765698107663,
       "Nucleotide GTR":0.06661490534189227,
       "RELAX alternative":0.07252374836036582,
       "RELAX null":0.0734705682786943,
       "RELAX partitioned descriptive":0.0757525093290258,
       "k (general descriptive)":1.316568267879453,
       "original name":"Rat"
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     "RhMonkey":{
       "General descriptive":0.003672848089716511,
       "MG94xREV with separate rates for branch sets":0.003717350789869306,
       "Nucleotide GTR":0.003778804730491441,
       "RELAX alternative":0.003633278464154418,
       "RELAX null":0.003661271320845124,
       "RELAX partitioned descriptive":0.003625957794514879,
       "k (general descriptive)":5.196295069596697,
       "original name":"RhMonkey"
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   "attributes":{
     "General descriptive":{
       "attribute type":"branch length",
       "display order":4
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     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
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     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
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     "RELAX alternative":{
       "attribute type":"branch length",
       "display order":2
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     "RELAX null":{
       "attribute type":"branch length",
       "display order":3
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     "RELAX partitioned descriptive":{
       "attribute type":"branch length",
       "display order":5
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     "k (general descriptive)":{
       "attribute type":"branch label",
       "display order":4
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     "original name":{
       "attribute type":"node label",
       "display order":-1
      }
    }
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 "data partitions":{
   "0":{
     "coverage":      [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 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] 
      ],
     "name":"relax.filter.default"
    }
  },
 "fits":{
   "General descriptive":{
     "AIC-c":6945.892677835464,
     "Log Likelihood":-3420.487593043145,
     "Rate Distributions":{
       "Shared":{
         "0":{
           "omega":2.201451464048879e-18,
           "proportion":0.3073650505039141
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         "1":{
           "omega":2.201451464048879e-18,
           "proportion":0.2383891488636319
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         "2":{
           "omega":2.201451281679838,
           "proportion":0.4542458006324541
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     "display order":4,
     "estimated parameters":51
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   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6987.566513560764,
     "Equilibrium frequencies":      [
[0.04876086397632926],
      [0.03982224127745371],
      [0.0494959405650269],
      [0.04152830682371345],
      [0.01810345074594235],
      [0.01478480742075003],
      [0.01837636270304883],
      [0.01541821854326533],
      [0.01892910005547028],
      [0.01545910240515689],
      [0.01921445878706794],
      [0.01612140169177368],
      [0.02829747763884322],
      [0.02311011106415996],
      [0.02872406592369408],
      [0.02410019507229243],
      [0.01663805943190806],
      [0.01358804506433061],
      [0.01688888041768248],
      [0.01417018446135155],
      [0.006177213955434187],
      [0.005044834822351987],
      [0.006270336287397383],
      [0.00526096577332031],
      [0.006458939937330408],
      [0.005274916061901906],
      [0.006556309326397028],
      [0.005500904159606446],
      [0.009655594186286731],
      [0.007885574003572761],
      [0.009801153568494354],
      [0.008223407979974132],
      [0.03327785448210915],
      [0.02717750758119989],
      [0.03377952261833742],
      [0.02834184710178207],
      [0.01235507229404208],
      [0.01009019590244688],
      [0.01254132667213156],
      [0.01052248035033209],
      [0.01291855364640413],
      [0.01055038238273567],
      [0.01311330258173711],
      [0.01100238215235291],
      [0.01931219560697892],
      [0.0157719705998612],
      [0.01960332955558842],
      [0.01644767379420349],
      [0.01965132601881859],
      [0.02049322866376102],
      [0.008933621043463411],
      [0.007295949736387736],
      [0.009068296583349953],
      [0.007608523013862737],
      [0.007628698224327205],
      [0.009481877006094248],
      [0.00795552712159237],
      [0.01396413011303752],
      [0.01140428846505027],
      [0.01417464125436193],
      [0.01189287130232129] 
      ],
     "Log Likelihood":-3461.208406480981,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *Reference*":        [
[0.7685912547191639, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *Test*":        [
[1.603198088111489, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":32
    },
   "Nucleotide GTR":{
     "AIC-c":7112.857288723968,
     "Equilibrium frequencies":      [
[0.3592490842490842],
      [0.181959706959707],
      [0.240018315018315],
      [0.2187728937728937] 
      ],
     "Log Likelihood":-3532.321213744258,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
       "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
       "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
       "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
      },
     "display order":0,
     "estimated parameters":24
    },
   "RELAX alternative":{
     "AIC-c":6931.926773483473,
     "Log Likelihood":-3429.236709163995,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":1.761161171239182e-19,
           "proportion":0.2691773911207853
          },
         "1":{
           "omega":1.762922332410267e-19,
           "proportion":0.2692122656891806
          },
         "2":{
           "omega":2.208286837998088,
           "proportion":0.4616103431900341
          }
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       "Test":{
         "0":{
           "omega":1.673670300056362e-44,
           "proportion":0.2691773911207853
          },
         "1":{
           "omega":1.677579612236672e-44,
           "proportion":0.2692122656891806
          },
         "2":{
           "omega":6.354762788556926,
           "proportion":0.4616103431900341
          }
        }
      },
     "display order":2,
     "estimated parameters":36
    },
   "RELAX null":{
     "AIC-c":6946.648596594286,
     "Log Likelihood":-3437.63727539638,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":1.408928936991542e-20,
           "proportion":0.265244047162938
          },
         "1":{
           "omega":1.410337865928411e-20,
           "proportion":0.28512630848952
          },
         "2":{
           "omega":3.213510017765925,
           "proportion":0.4496296443475419
          }
        },
       "Test":{
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           "omega":1.408928936991542e-20,
           "proportion":0.265244047162938
          },
         "1":{
           "omega":1.410337865928411e-20,
           "proportion":0.28512630848952
          },
         "2":{
           "omega":3.213510017765925,
           "proportion":0.4496296443475419
          }
        }
      },
     "display order":3,
     "estimated parameters":35
    },
   "RELAX partitioned descriptive":{
     "AIC-c":6937.049237937651,
     "Log Likelihood":-3427.627954124649,
     "Rate Distributions":{
       "Reference":{
         "0":{
           "omega":0.1847557016619168,
           "proportion":0.4766160247339328
          },
         "1":{
           "omega":0.3367540359539261,
           "proportion":0.3005513276312735
          },
         "2":{
           "omega":4.272816072857538,
           "proportion":0.2228326476347937
          }
        },
       "Test":{
         "0":{
           "omega":1.127143149593234e-21,
           "proportion":0.2367540589657237
          },
         "1":{
           "omega":1.128270292740756e-21,
           "proportion":0.2771164325302933
          },
         "2":{
           "omega":6.023626417874829,
           "proportion":0.4861295085039831
          }
        }
      },
     "display order":5,
     "estimated parameters":40
    }
  },
 "input":{
   "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",
   "number of sequences":10,
   "number of sites":187,
   "partition count":1,
   "trees":{
     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
    }
  },
 "runtime":"2.5.32",
 "test results":{
   "LRT":16.80113246476958,
   "p-value":4.150852429507523e-05,
   "relaxation or intensification parameter":2.334214628944839
  },
 "tested":{
   "0":{
     "Baboon":"Reference",
     "Cat":"Test",
     "Chimp":"Reference",
     "Cow":"Test",
     "Horse":"Test",
     "Human":"Reference",
     "Mouse":"Reference",
     "Node1":"Reference",
     "Node12":"Reference",
     "Node2":"Reference",
     "Node3":"Reference",
     "Node8":"Reference",
     "Node9":"Reference",
     "Pig":"Reference",
     "Rat":"Reference",
     "RhMonkey":"Reference"
    }
  },
 "timers":{
   "General descriptive model fitting":{
     "order":2,
     "timer":127
    },
   "Overall":{
     "order":0,
     "timer":396
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":8
    },
   "RELAX alternative model fitting":{
     "order":3,
     "timer":103
    },
   "RELAX null model fitting":{
     "order":4,
     "timer":41
    },
   "RELAX partitioned descriptive":{
     "order":5,
     "timer":116
    }
  }
}