annotate test-data/busted-out1.json @ 27:8c388fd08c09 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2063bc1f8f9cb97de147b86dbe9189fc496b206a"

{
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  ],
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond",
   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
   "contact":"[e-mail]",
   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
   "version":"3.1"
  },
 "background":0,
 "branch attributes":{
   "0":{
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       "MG94xREV with separate rates for branch sets":0.001772434847524003,
       "Nucleotide GTR":0.001680040630127455,
       "constrained":0.001513413708231178,
       "original name":"Baboon",
       "unconstrained":0.00161713005248515
      },
     "Cat":{
       "MG94xREV with separate rates for branch sets":0.2735065373507703,
       "Nucleotide GTR":0.2660909938917123,
       "constrained":0.3466844629529476,
       "original name":"Cat",
       "unconstrained":0.3607268493024173
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     "Chimp":{
       "MG94xREV with separate rates for branch sets":0.001828401123834132,
       "Nucleotide GTR":0.001818373670119325,
       "constrained":0.001854421055569225,
       "original name":"Chimp",
       "unconstrained":0.001853794709397617
      },
     "Cow":{
       "MG94xREV with separate rates for branch sets":0.2477981038577003,
       "Nucleotide GTR":0.2481025999892287,
       "constrained":0.3115800338446564,
       "original name":"Cow",
       "unconstrained":0.3266266518611717
      },
     "Horse":{
       "MG94xREV with separate rates for branch sets":0.21116782461044,
       "Nucleotide GTR":0.2090310577070883,
       "constrained":0.2473423214593362,
       "original name":"Horse",
       "unconstrained":0.2568895651944081
      },
     "Human":{
       "MG94xREV with separate rates for branch sets":0,
       "Nucleotide GTR":0,
       "constrained":0,
       "original name":"Human",
       "unconstrained":0
      },
     "Mouse":{
       "MG94xREV with separate rates for branch sets":0.1200804161847832,
       "Nucleotide GTR":0.1180171198334285,
       "constrained":0.1381882260320684,
       "original name":"Mouse",
       "unconstrained":0.1482500840848965
      },
     "Node1":{
       "MG94xREV with separate rates for branch sets":0.2841417945012228,
       "Nucleotide GTR":0.2767237570684924,
       "constrained":0.3893703941610758,
       "unconstrained":0.4535373691584812
      },
     "Node12":{
       "MG94xREV with separate rates for branch sets":0.01789005959388253,
       "Nucleotide GTR":0.01784803874223016,
       "constrained":0.01603697675468384,
       "unconstrained":0.01716581823757766
      },
     "Node2":{
       "MG94xREV with separate rates for branch sets":0.06425321743363792,
       "Nucleotide GTR":0.06613162123865737,
       "constrained":0.06766882319669908,
       "unconstrained":0.06748821329187271
      },
     "Node3":{
       "MG94xREV with separate rates for branch sets":0.1017634409613201,
       "Nucleotide GTR":0.09886326330774685,
       "constrained":0.128627313187861,
       "unconstrained":0.1385358286963005
      },
     "Node8":{
       "MG94xREV with separate rates for branch sets":0.1095532710088725,
       "Nucleotide GTR":0.106239268140425,
       "constrained":0.1326559254556453,
       "unconstrained":0.1430782720540034
      },
     "Node9":{
       "MG94xREV with separate rates for branch sets":0.02590764371262369,
       "Nucleotide GTR":0.02566573875750134,
       "constrained":0.02991066003065707,
       "unconstrained":0.02952913741456189
      },
     "Pig":{
       "MG94xREV with separate rates for branch sets":0.1925158663261413,
       "Nucleotide GTR":0.1871893456388788,
       "constrained":0.2351007649069627,
       "original name":"Pig",
       "unconstrained":0.248176820169511
      },
     "Rat":{
       "MG94xREV with separate rates for branch sets":0.06699144002108472,
       "Nucleotide GTR":0.06661283005976348,
       "constrained":0.06832918896283274,
       "original name":"Rat",
       "unconstrained":0.07114161288708017
      },
     "RhMonkey":{
       "MG94xREV with separate rates for branch sets":0.003716234330029482,
       "Nucleotide GTR":0.003775170135617877,
       "constrained":0.004078975866589158,
       "original name":"RhMonkey",
       "unconstrained":0.003977618821878279
      }
    },
   "attributes":{
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "constrained":{
       "attribute type":"branch length",
       "display order":1
      },
     "original name":{
       "attribute type":"node label",
       "display order":0
      },
     "unconstrained":{
       "attribute type":"branch length",
       "display order":0
      }
    }
  },
 "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":"busted.filter.default"
    }
  },
 "fits":{
   "Constrained model":{
     "AIC-c":6918.865252134614,
     "Log Likelihood":-3419.580167050914,
     "Rate Distributions":{
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.3286044813984554,
           "rate":0.3114745230555425
          },
         "1":{
           "proportion":0.5759073485616787,
           "rate":1.038727366194607
          },
         "2":{
           "proportion":0.09548817003986594,
           "rate":3.135858111155513
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.1610337459523823
          },
         "1":{
           "omega":0.9239856235614761,
           "proportion":0
          },
         "2":{
           "omega":1,
           "proportion":0.8389662540476177
          }
        }
      },
     "display order":3,
     "estimated parameters":39
    },
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":6997.104847699299,
     "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":-3467.012706765863,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.9959842858928788, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":31
    },
   "Nucleotide GTR":{
     "AIC-c":7112.857310169033,
     "Equilibrium frequencies":      [
[0.3592490842490842],
      [0.181959706959707],
      [0.240018315018315],
      [0.2187728937728937] 
      ],
     "Log Likelihood":-3532.32122446679,
     "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":0.2647746107611847,
       "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
       "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
       "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
      },
     "display order":0,
     "estimated parameters":24
    },
   "Unconstrained model":{
     "AIC-c":6910.776988890891,
     "Log Likelihood":-3414.491829601268,
     "Rate Distributions":{
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.2655037162058198,
           "rate":0.2749303122566129
          },
         "1":{
           "proportion":0.6321791898264187,
           "rate":0.9740711294478059
          },
         "2":{
           "proportion":0.1023170939677615,
           "rate":3.041695877803997
          }
        },
       "Test":{
         "0":{
           "omega":0,
           "proportion":0.386646389823596
          },
         "1":{
           "omega":0.9964438830494696,
           "proportion":0
          },
         "2":{
           "omega":1.876622752045829,
           "proportion":0.613353610176404
          }
        }
      },
     "display order":2,
     "estimated parameters":40
    }
  },
 "input":{
   "file name":"/tmp/tmpfqvtss8b/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)"
    }
  },
 "test results":{
   "LRT":10.17667489929045,
   "p-value":0.003084133210483175
  },
 "tested":{
   "0":{
     "Baboon":"test",
     "Cat":"test",
     "Chimp":"test",
     "Cow":"test",
     "Horse":"test",
     "Human":"test",
     "Mouse":"test",
     "Node1":"test",
     "Node12":"test",
     "Node2":"test",
     "Node3":"test",
     "Node8":"test",
     "Node9":"test",
     "Pig":"test",
     "Rat":"test",
     "RhMonkey":"test"
    }
  },
 "timers":{
   "Constrained BUSTED model fitting":{
     "order":3,
     "timer":70
    },
   "Overall":{
     "order":0,
     "timer":451
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":10
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":370
    }
  }
}