diff test-data/relax-out2-1.json @ 9:3ea647006f17 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:16:40 +0000
parents f6e7b5955712
children 6761212b7f1d
line wrap: on
line diff
--- a/test-data/relax-out2-1.json	Sat Nov 27 11:30:35 2021 +0000
+++ b/test-data/relax-out2-1.json	Wed Mar 30 00:16:40 2022 +0000
@@ -1,60 +1,60 @@
 {
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-       "k (general descriptive)":2.315896411158361,
+       "General descriptive":0.3649705108927348,
+       "MG94xREV with separate rates for branch sets":0.2761191158060541,
+       "Nucleotide GTR":0.2660536011315811,
+       "RELAX alternative":0.3757111787573828,
+       "RELAX null":0.360767755751942,
+       "RELAX partitioned descriptive":0.3768226672635935,
+       "k (general descriptive)":2.322824217601444,
        "original name":"CAT"
       },
      "CHIMP":{
-       "General descriptive":0.001848668319765628,
-       "MG94xREV with separate rates for branch sets":0.001822931846626064,
-       "Nucleotide GTR":0.001818373670119325,
-       "RELAX alternative":0.00185493617203229,
-       "RELAX null":0.001854095610530333,
-       "RELAX partitioned descriptive":0.00185387819029751,
-       "k (general descriptive)":5.254528914257314,
+       "General descriptive":0.001848544328521468,
+       "MG94xREV with separate rates for branch sets":0.001822551054713939,
+       "Nucleotide GTR":0.001820258053351119,
+       "RELAX alternative":0.001854643673065862,
+       "RELAX null":0.00185572990722179,
+       "RELAX partitioned descriptive":0.001854201499317722,
+       "k (general descriptive)":5.263917013225917,
        "original name":"CHIMP"
       },
      "COW":{
-       "General descriptive":0.3732204271616263,
-       "MG94xREV with separate rates for branch sets":0.2488439658756959,
-       "Nucleotide GTR":0.2481025999892287,
-       "RELAX alternative":0.3383682965197552,
-       "RELAX null":0.3267413510264365,
-       "RELAX partitioned descriptive":0.3368059806284254,
-       "k (general descriptive)":2.844135916463983,
+       "General descriptive":0.3734992963367884,
+       "MG94xREV with separate rates for branch sets":0.248802707042435,
+       "Nucleotide GTR":0.2480198736772598,
+       "RELAX alternative":0.3379561449590825,
+       "RELAX null":0.3268684624461423,
+       "RELAX partitioned descriptive":0.336296078659758,
+       "k (general descriptive)":2.847745204182733,
        "original name":"COW"
       },
      "HORSE":{
-       "General descriptive":0.2802894874897226,
-       "MG94xREV with separate rates for branch sets":0.2115283499416638,
-       "Nucleotide GTR":0.2090310577070883,
-       "RELAX alternative":0.263552542851074,
-       "RELAX null":0.2568271402938284,
-       "RELAX partitioned descriptive":0.262017696350779,
-       "k (general descriptive)":1.928668982186118,
+       "General descriptive":0.2805104186424681,
+       "MG94xREV with separate rates for branch sets":0.2114983058912022,
+       "Nucleotide GTR":0.2090998951755368,
+       "RELAX alternative":0.2639982922145814,
+       "RELAX null":0.2570519477156736,
+       "RELAX partitioned descriptive":0.26200095593742,
+       "k (general descriptive)":1.930891329212253,
        "original name":"HORSE"
       },
      "HUMAN":{
@@ -64,101 +64,101 @@
        "RELAX alternative":0,
        "RELAX null":0,
        "RELAX partitioned descriptive":0,
-       "k (general descriptive)":1.458575021945062,
+       "k (general descriptive)":1.416548546052124,
        "original name":"HUMAN"
       },
      "MOUSE":{
-       "General descriptive":0.1308201891676921,
-       "MG94xREV with separate rates for branch sets":0.1193025698417779,
-       "Nucleotide GTR":0.1180171198334285,
-       "RELAX alternative":0.1517050531281043,
-       "RELAX null":0.1483289620283821,
-       "RELAX partitioned descriptive":0.1490164254890325,
-       "k (general descriptive)":0.4631708151770838,
+       "General descriptive":0.1308803878257961,
+       "MG94xREV with separate rates for branch sets":0.1192893635530923,
+       "Nucleotide GTR":0.1181058300538561,
+       "RELAX alternative":0.1516183081271659,
+       "RELAX null":0.1483567973872321,
+       "RELAX partitioned descriptive":0.1488950288407203,
+       "k (general descriptive)":0.4621316779775653,
        "original name":"MOUSE"
       },
      "Node1":{
-       "General descriptive":0.3501050632149825,
-       "MG94xREV with separate rates for branch sets":0.2890877742792198,
-       "Nucleotide GTR":0.2767237570684924,
-       "RELAX alternative":0.4255409853463661,
-       "RELAX null":0.4550463522153177,
-       "RELAX partitioned descriptive":0.4344852084340091,
-       "k (general descriptive)":0.4579130056597299
+       "General descriptive":0.3501143091462658,
+       "MG94xREV with separate rates for branch sets":0.2891531817656844,
+       "Nucleotide GTR":0.2767105173979571,
+       "RELAX alternative":0.420525835142383,
+       "RELAX null":0.4545405634998693,
+       "RELAX partitioned descriptive":0.4297776151561553,
+       "k (general descriptive)":0.4575702395890889
       },
      "Node12":{
-       "General descriptive":0.01766689355384354,
-       "MG94xREV with separate rates for branch sets":0.01757408524377322,
-       "Nucleotide GTR":0.01784803874223016,
-       "RELAX alternative":0.01676792601958491,
-       "RELAX null":0.01717214969820526,
-       "RELAX partitioned descriptive":0.01691268333643598,
-       "k (general descriptive)":0.124164332983979
+       "General descriptive":0.01766178787800134,
+       "MG94xREV with separate rates for branch sets":0.0175770110347634,
+       "Nucleotide GTR":0.01784222107494562,
+       "RELAX alternative":0.01626048141633729,
+       "RELAX null":0.01716868534229337,
+       "RELAX partitioned descriptive":0.01647240042293572,
+       "k (general descriptive)":0.124120594408151
       },
      "Node2":{
-       "General descriptive":0.0577170117416439,
-       "MG94xREV with separate rates for branch sets":0.06231584601001511,
-       "Nucleotide GTR":0.06613162123865737,
-       "RELAX alternative":0.0656020383942497,
-       "RELAX null":0.06749468776339668,
-       "RELAX partitioned descriptive":0.063727560710161,
-       "k (general descriptive)":0.5375515816350908
+       "General descriptive":0.05770266360624338,
+       "MG94xREV with separate rates for branch sets":0.06229443926236622,
+       "Nucleotide GTR":0.06614755778044307,
+       "RELAX alternative":0.06487498265124983,
+       "RELAX null":0.06743647945583151,
+       "RELAX partitioned descriptive":0.06330449773182804,
+       "k (general descriptive)":0.5360768532731082
       },
      "Node3":{
-       "General descriptive":0.1331109882486915,
-       "MG94xREV with separate rates for branch sets":0.1003158387194354,
-       "Nucleotide GTR":0.09886326330774685,
-       "RELAX alternative":0.1377575305960468,
-       "RELAX null":0.1387229575435225,
-       "RELAX partitioned descriptive":0.1370056132243871,
-       "k (general descriptive)":1.983651509686636
+       "General descriptive":0.1330256319960288,
+       "MG94xREV with separate rates for branch sets":0.1003154990002797,
+       "Nucleotide GTR":0.09883748387954429,
+       "RELAX alternative":0.1378173139909468,
+       "RELAX null":0.1387701954254672,
+       "RELAX partitioned descriptive":0.136719474302551,
+       "k (general descriptive)":1.981625732305646
       },
      "Node8":{
-       "General descriptive":0.1404566834691408,
-       "MG94xREV with separate rates for branch sets":0.1126868091796008,
-       "Nucleotide GTR":0.106239268140425,
-       "RELAX alternative":0.1456361998411515,
-       "RELAX null":0.1432141493320635,
-       "RELAX partitioned descriptive":0.1499980670367906,
-       "k (general descriptive)":2.210307133212389
+       "General descriptive":0.1404338383825282,
+       "MG94xREV with separate rates for branch sets":0.1127066220459272,
+       "Nucleotide GTR":0.1062201244057951,
+       "RELAX alternative":0.1439313895033506,
+       "RELAX null":0.14318831284655,
+       "RELAX partitioned descriptive":0.1481785335086442,
+       "k (general descriptive)":2.211998835217187
       },
      "Node9":{
-       "General descriptive":0.0266459915750866,
-       "MG94xREV with separate rates for branch sets":0.02627629459000785,
-       "Nucleotide GTR":0.02566573875750134,
-       "RELAX alternative":0.02987801750435297,
-       "RELAX null":0.02953491567444994,
-       "RELAX partitioned descriptive":0.02997035035825657,
-       "k (general descriptive)":0.07328040064262234
+       "General descriptive":0.02665501999328081,
+       "MG94xREV with separate rates for branch sets":0.02627402966233569,
+       "Nucleotide GTR":0.02567813733543303,
+       "RELAX alternative":0.02985671529404269,
+       "RELAX null":0.02953553824738531,
+       "RELAX partitioned descriptive":0.02996950192160838,
+       "k (general descriptive)":0.07343805012797726
       },
      "PIG":{
-       "General descriptive":0.2103978170052953,
-       "MG94xREV with separate rates for branch sets":0.1921267861604921,
-       "Nucleotide GTR":0.1871893456388788,
-       "RELAX alternative":0.2514899807955971,
-       "RELAX null":0.2481060168445591,
-       "RELAX partitioned descriptive":0.251294309938668,
-       "k (general descriptive)":1.57905583202459,
+       "General descriptive":0.2105401970679286,
+       "MG94xREV with separate rates for branch sets":0.1921302603267553,
+       "Nucleotide GTR":0.1871390433004313,
+       "RELAX alternative":0.2517917117490165,
+       "RELAX null":0.2483169436500481,
+       "RELAX partitioned descriptive":0.2506475053874151,
+       "k (general descriptive)":1.582105640200874,
        "original name":"PIG"
       },
      "RAT":{
-       "General descriptive":0.07161013387643886,
-       "MG94xREV with separate rates for branch sets":0.06830746072347418,
-       "Nucleotide GTR":0.06661283005976348,
-       "RELAX alternative":0.07293805936494982,
-       "RELAX null":0.07115038941652747,
-       "RELAX partitioned descriptive":0.07467247582140474,
-       "k (general descriptive)":1.319839560623237,
+       "General descriptive":0.07158272879959397,
+       "MG94xREV with separate rates for branch sets":0.06831927364558048,
+       "Nucleotide GTR":0.06661490534189227,
+       "RELAX alternative":0.07311180317129368,
+       "RELAX null":0.07112698282214641,
+       "RELAX partitioned descriptive":0.07451416024404128,
+       "k (general descriptive)":1.317928928374736,
        "original name":"RAT"
       },
      "RHMONKEY":{
-       "General descriptive":0.003674114425886965,
-       "MG94xREV with separate rates for branch sets":0.003753885794232333,
-       "Nucleotide GTR":0.003775170135617877,
-       "RELAX alternative":0.004180662465434332,
-       "RELAX null":0.003978610819466039,
-       "RELAX partitioned descriptive":0.004190519057865823,
-       "k (general descriptive)":5.183560186695944,
+       "General descriptive":0.003673715052669516,
+       "MG94xREV with separate rates for branch sets":0.003755247927570558,
+       "Nucleotide GTR":0.003778804730491441,
+       "RELAX alternative":0.004176749981889291,
+       "RELAX null":0.00397871921631754,
+       "RELAX partitioned descriptive":0.004188079354984015,
+       "k (general descriptive)":5.301456309232226,
        "original name":"RHMONKEY"
       }
     },
@@ -207,21 +207,21 @@
   },
  "fits":{
    "General descriptive":{
-     "AIC-c":6945.891070751259,
-     "Log Likelihood":-3420.486789501042,
+     "AIC-c":6945.886057024934,
+     "Log Likelihood":-3420.484282637879,
      "Rate Distributions":{
        "Shared":{
          "0":{
-           "omega":2.20271427504516e-18,
-           "proportion":0.00789425874100967
+           "omega":2.201373594751134e-18,
+           "proportion":0.5258178735075876
           },
          "1":{
-           "omega":2.20271427504516e-18,
-           "proportion":0.5381203586928067
+           "omega":2.201373594751134e-18,
+           "proportion":0.01992025780064184
           },
          "2":{
-           "omega":2.202714092571507,
-           "proportion":0.4539853825661836
+           "omega":2.201373412388544,
+           "proportion":0.4542618686917706
           }
         }
       },
@@ -229,7 +229,7 @@
      "estimated parameters":51
     },
    "MG94xREV with separate rates for branch sets":{
-     "AIC-c":6987.278662183248,
+     "AIC-c":6987.278076404838,
      "Equilibrium frequencies":      [
 [0.04876086397632926],
       [0.03982224127745371],
@@ -293,177 +293,177 @@
       [0.01417464125436193],
       [0.01189287130232129] 
       ],
-     "Log Likelihood":-3461.064480792223,
+     "Log Likelihood":-3461.064187903018,
      "Rate Distributions":{
        "non-synonymous/synonymous rate ratio for *Reference*":        [
-[1.240656122625563, 1] 
+[1.243401858007084, 1] 
         ],
        "non-synonymous/synonymous rate ratio for *Test*":        [
-[0.5611761689874598, 1] 
+[0.5612874934764923, 1] 
         ]
       },
      "display order":1,
      "estimated parameters":32
     },
    "Nucleotide GTR":{
-     "AIC-c":7112.857310169033,
+     "AIC-c":7112.857288723968,
      "Equilibrium frequencies":      [
 [0.3592490842490842],
       [0.181959706959707],
       [0.240018315018315],
       [0.2187728937728937] 
       ],
-     "Log Likelihood":-3532.32122446679,
+     "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":0.2647746107611847,
-       "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
+       "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":6901.392449196474,
-     "Log Likelihood":-3408.754211469135,
+     "AIC-c":6909.668413948684,
+     "Log Likelihood":-3408.69933855329,
      "Rate Distributions":{
        "Reference":{
          "0":{
            "omega":0,
-           "proportion":0.3814061972635792
+           "proportion":0.3825895192221547
           },
          "1":{
-           "omega":0.4330262245823013,
+           "omega":0.003503464580598538,
            "proportion":0
           },
          "2":{
-           "omega":2.405594515133199,
-           "proportion":0.6185938027364208
+           "omega":2.417572962231385,
+           "proportion":0.6174104807778453
           }
         },
        "Synonymous site-to-site rates":{
          "0":{
-           "proportion":0.2800901562602482,
-           "rate":0.2837970682663188
+           "proportion":0.2789425737851868,
+           "rate":0.2834765074731829
           },
          "1":{
-           "proportion":0.6272754947629234,
-           "rate":0.9947075941569237
+           "proportion":0.6311785441975573,
+           "rate":0.9970973177052372
           },
          "2":{
-           "proportion":0.09263434897682828,
-           "rate":3.20135608237551
+           "proportion":0.089878882017256,
+           "rate":3.244142488658602
           }
         },
        "Test":{
          "0":{
            "omega":0,
-           "proportion":0.3814061972635792
+           "proportion":0.3825895192221547
           },
          "1":{
-           "omega":0.9999750044281671,
+           "omega":0.9998114377116485,
            "proportion":0
           },
          "2":{
-           "omega":1.00002621592498,
-           "proportion":0.6185938027364208
+           "omega":1.000029443594731,
+           "proportion":0.6174104807778453
           }
         }
       },
      "display order":2,
-     "estimated parameters":41
+     "estimated parameters":45
     },
    "RELAX null":{
-     "AIC-c":6910.777215627525,
-     "Log Likelihood":-3414.491942969586,
+     "AIC-c":6919.152853316747,
+     "Log Likelihood":-3414.491495151524,
      "Rate Distributions":{
        "Reference":{
          "0":{
            "omega":0,
-           "proportion":0.04600287725570656
+           "proportion":0.3885051761591228
           },
          "1":{
-           "omega":0,
-           "proportion":0.3432466763494891
+           "omega":0.9958737025997172,
+           "proportion":0
           },
          "2":{
-           "omega":1.896477292815783,
-           "proportion":0.6107504463948045
+           "omega":1.887643080900262,
+           "proportion":0.6114948238408772
           }
         },
        "Synonymous site-to-site rates":{
          "0":{
-           "proportion":0.2641095265325168,
-           "rate":0.2744837794048847
+           "proportion":0.2642938080646302,
+           "rate":0.2741590488311177
           },
          "1":{
-           "proportion":0.6330324513232739,
-           "rate":0.9729462345446451
+           "proportion":0.633162055223991,
+           "rate":0.9728788992663913
           },
          "2":{
-           "proportion":0.1028580221442092,
-           "rate":3.029415427453047
+           "proportion":0.1025441367113787,
+           "rate":3.038218152856258
           }
         },
        "Test":{
          "0":{
            "omega":0,
-           "proportion":0.04600287725570656
+           "proportion":0.3885051761591228
           },
          "1":{
-           "omega":0,
-           "proportion":0.3432466763494891
+           "omega":0.9958737025997172,
+           "proportion":0
           },
          "2":{
-           "omega":1.896477292815783,
-           "proportion":0.6107504463948045
+           "omega":1.887643080900262,
+           "proportion":0.6114948238408772
           }
         }
       },
      "display order":3,
-     "estimated parameters":40
+     "estimated parameters":44
     },
    "RELAX partitioned descriptive":{
-     "AIC-c":6909.42794543134,
-     "Log Likelihood":-3408.579104294618,
+     "AIC-c":6917.810941882631,
+     "Log Likelihood":-3408.559317095162,
      "Rate Distributions":{
        "Reference":{
          "0":{
-           "omega":0.05035684771569529,
-           "proportion":0.3805224005150026
+           "omega":0.03550460650841439,
+           "proportion":0.354985198548996
           },
          "1":{
-           "omega":0.07013486723985318,
-           "proportion":0.003462124163764896
+           "omega":0.05439939847728128,
+           "proportion":0.02231130867735708
           },
          "2":{
-           "omega":2.344944921144001,
-           "proportion":0.6160154753212325
+           "omega":2.333762420535514,
+           "proportion":0.6227034927736469
           }
         },
        "Test":{
          "0":{
            "omega":0,
-           "proportion":0.03160127773820932
+           "proportion":0.3705590531463396
           },
          "1":{
            "omega":0,
-           "proportion":0.4079248249859382
+           "proportion":0.06265340406614885
           },
          "2":{
-           "omega":1.11269394570475,
-           "proportion":0.5604738972758525
+           "omega":1.08372848194659,
+           "proportion":0.5667875427875115
           }
         }
       },
      "display order":5,
-     "estimated parameters":45
+     "estimated parameters":49
     }
   },
  "input":{
-   "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/5/working/./input.nex",
+   "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex",
    "number of sequences":10,
    "number of sites":187,
    "partition count":1,
@@ -471,10 +471,11 @@
      "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":11.47546300090198,
-   "p-value":0.0007052107640865835,
-   "relaxation or intensification parameter":2.986519568748539e-05
+   "LRT":11.58431319646934,
+   "p-value":0.0006651049394417186,
+   "relaxation or intensification parameter":3.335337302186161e-05
   },
  "tested":{
    "0":{
@@ -499,11 +500,11 @@
  "timers":{
    "General descriptive model fitting":{
      "order":2,
-     "timer":127
+     "timer":105
     },
    "Overall":{
      "order":0,
-     "timer":645
+     "timer":3013
     },
    "Preliminary model fitting":{
      "order":1,
@@ -511,15 +512,15 @@
     },
    "RELAX alternative model fitting":{
      "order":3,
-     "timer":178
+     "timer":1229
     },
    "RELAX null model fitting":{
      "order":4,
-     "timer":115
+     "timer":690
     },
    "RELAX partitioned descriptive":{
      "order":5,
-     "timer":216
+     "timer":980
     }
   }
 }
\ No newline at end of file