Mercurial > repos > iuc > hyphy_summary
diff test-data/relax-out2-1.json @ 7:f3e408cc2546 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
| author | iuc |
|---|---|
| date | Thu, 18 Aug 2022 13:50:20 +0000 |
| parents | 81b23515db14 |
| children |
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--- a/test-data/relax-out2-1.json Wed Mar 30 00:23:34 2022 +0000 +++ b/test-data/relax-out2-1.json Thu Aug 18 13:50:20 2022 +0000 @@ -1,60 +1,55 @@ { - "Synonymous site-posteriors": [ -[0.6636913410863983, 0.4162861463391083, 0.4207669648198341, 0.5266957556553843, 0.7895328001950979, 0.9272590205679656, 0.6152945530195142, 0.7578515907144813, 0.1238947876214084, 0.3018037085532145, 0.2282864078469784, 0.7937331893941735, 0.5320234040808555, 0.4706871966418729, 0.5439405260809865, 0.1517881809649885, 0.09043162428247122, 0.08685065723885507, 0.03885767834229433, 0.05375215759679093, 0.1268225432845697, 0.07577668231270167, 0.6052751007842404, 0.2502160552371602, 0.2736708121460947, 0.7706988555442902, 0.748841088623575, 0.5723843790763415, 0.8949826459565234, 0.6384606763319275, 0.8239292808797724, 0.1664437117300734, 0.06847586601224155, 0.8824121911043322, 0.1271766673209644, 0.1148021398435604, 0.4117122840037579, 0.406499277480147, 0.4008888256405372, 0.8646423634969567, 0.8190691829853963, 0.500042208706628, 0.06797606990283254, 0.8587865476515109, 0.2593957205794197, 0.9238491908671513, 0.8512119846143551, 0.3063762561200102, 0.6669337037749883, 0.8301646821437867, 0.636853262388444, 0.2905505446517289, 0.241935494101366, 0.8128255914518664, 0.8694325465217606, 0.848675874090462, 0.7267309584033903, 0.6911098971620047, 0.583052312866751, 0.7867301296752277, 0.8804662810822645, 0.809644890871663, 0.3376753254168838, 0.8283707254597538, 0.4508845830660299, 0.0216331593168105, 0.3776212213040052, 0.07931015513156162, 0.2950308574589764, 0.1222844084424193, 0.2323128587705404, 0.8289275512891175, 0.631178544197552, 0.05325361766368054, 0.8662251485184755, 0.3212301783117932, 0.861017744903573, 0.5761459249816555, 0.7343170662946317, 0.09741215372980042, 0.1807849329793456, 0.4569927206185401, 0.1643327673634512, 0.1185284443150185, 0.7324030664891016, 0.8472376168908595, 0.8234507825433042, 0.3173650640633187, 0.9292941067446137, 0.2735709551124761, 0.06276324502006964, 0.8863623602779909, 0.8489458938246637, 0.9130985854899469, 0.2797994574222102, 0.9075929417789967, 0.5150137541063844, 0.6723801037322925, 0.06367665954274145, 0.7320704660828672, 0.3527697452184735, 0.8461914351678148, 0.1351211810935134, 0.4613328492603073, 0.124276342334713, 0.8475110259360163, 0.06206865929630392, 0.04122997041189784, 0.8672530362064098, 0.4581644690927911, 0.8415744872053624, 0.1236376392825715, 0.9203127839835408, 0.1271766673209644, 0.8695568439105728, 0.3242726536321666, 0.6064715811235907, 0.1165318836810881, 0.8722046458122451, 0.2149812075751182, 0.0665951965283386, 0.2742588346922531, 0.3653273246144033, 0.721568903142608, 0.2413820620693605, 0.588103471777193, 0.8686043286753734, 0.08010632672074527, 0.5761580378346324, 0.523544810651528, 0.7668186650136124, 0.731052877850959, 0.329467117190821, 0.3208367729701002, 0.06144214634573335, 0.8062919404136638, 0.6220061302015701, 0.2090699504697991, 0.9185889308419551, 0.7767477941019779, 0.5356868588016898, 0.8031407570629746, 0.9042937966352298, 0.7393000429370805, 0.5400823150565389, 0.7357099400943075, 0.9523857813416914, 0.1564516235889077, 0.4882755555291234, 0.1252145971401747, 0.9240797408523314, 0.3440045440887274, 0.2962312024479645, 0.7573666819357475, 0.8253574958581319, 0.1229691454797458, 0.5683960261123714, 0.8313273153092753, 0.8469672878626771, 0.9486952624246412, 0.9172349146810788, 0.3831591722552873, 0.1357178596976572, 0.363473489194153, 0.9082063423261078, 0.7310413241232628, 0.8851632091676694, 0.04945472390779559, 0.7711621490316225, 0.05488172075128287, 0.5228323482367553, 0.9173152634471772, 0.5124114157230398, 0.346256158312588, 0.6630870619405116, 0.9355504393694619, 0.7330631304859381, 0.8707601306551315, 0.7291701265889592, 0.8821257366537769, 0.04095247534309823, 0.557046605833562, 0.2622389511630402, 0.6288683743714585, 0.02357245006214095, 0.01713741578412558, 0.6313826523714624], - 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"RELAX alternative":0.1378173139909468, - "RELAX null":0.1387701954254672, - "RELAX partitioned descriptive":0.136719474302551, - "k (general descriptive)":1.981625732305646 + "RELAX alternative":0.1265135269643693, + "RELAX null":0.1276253046950155, + "RELAX partitioned descriptive":0.1271876163104063, + "k (general descriptive)":1.981364628056296 }, "Node8":{ - "General descriptive":0.1404338383825282, + "General descriptive":0.140369727816558, "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 + "RELAX alternative":0.1280322211601967, + "RELAX null":0.1343412714385626, + "RELAX partitioned descriptive":0.1406663540457613, + "k (general descriptive)":2.211767324109487 }, "Node9":{ - "General descriptive":0.02665501999328081, + "General descriptive":0.02663291940160552, "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 + "RELAX alternative":0.02720907734174326, + "RELAX null":0.02752483699250281, + "RELAX partitioned descriptive":0.02810928828288993, + "k (general descriptive)":0.07329530197274074 }, "PIG":{ - "General descriptive":0.2105401970679286, + "General descriptive":0.2104965149960229, "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, + "RELAX alternative":0.2174541263946326, + "RELAX null":0.2166570805170097, + "RELAX partitioned descriptive":0.2198382730708073, + "k (general descriptive)":1.581624239713873, "original name":"PIG" }, "RAT":{ - "General descriptive":0.07158272879959397, + "General descriptive":0.07156643194841542, "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, + "RELAX alternative":0.07273892007491474, + "RELAX null":0.07342001791171293, + "RELAX partitioned descriptive":0.07588524426470618, + "k (general descriptive)":1.318666444029934, "original name":"RAT" }, "RHMONKEY":{ - "General descriptive":0.003673715052669516, + "General descriptive":0.003670942377703963, "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, + "RELAX alternative":0.003673289414323487, + "RELAX null":0.003666197747079884, + "RELAX partitioned descriptive":0.003661285250492945, + "k (general descriptive)":5.244027200799457, "original name":"RHMONKEY" } }, @@ -207,21 +202,21 @@ }, "fits":{ "General descriptive":{ - "AIC-c":6945.886057024934, - "Log Likelihood":-3420.484282637879, + "AIC-c":6945.887251511141, + "Log Likelihood":-3420.484879880983, "Rate Distributions":{ "Shared":{ "0":{ - "omega":2.201373594751134e-18, - "proportion":0.5258178735075876 + "omega":2.201644423775106e-18, + "proportion":0.1667516969215508 }, "1":{ - "omega":2.201373594751134e-18, - "proportion":0.01992025780064184 + "omega":2.201644423775106e-18, + "proportion":0.3790423141178453 }, "2":{ - "omega":2.201373412388544, - "proportion":0.4542618686917706 + "omega":2.201644241390081, + "proportion":0.4542059889606039 } } }, @@ -326,144 +321,116 @@ "estimated parameters":24 }, "RELAX alternative":{ - "AIC-c":6909.668413948684, - "Log Likelihood":-3408.69933855329, + "AIC-c":6938.419285358699, + "Log Likelihood":-3432.482965101608, "Rate Distributions":{ "Reference":{ "0":{ "omega":0, - "proportion":0.3825895192221547 + "proportion":0.2968543549269862 }, "1":{ - "omega":0.003503464580598538, - "proportion":0 + "omega":0, + "proportion":0.2447083724876047 }, "2":{ - "omega":2.417572962231385, - "proportion":0.6174104807778453 - } - }, - "Synonymous site-to-site rates":{ - "0":{ - "proportion":0.2789425737851868, - "rate":0.2834765074731829 - }, - "1":{ - "proportion":0.6311785441975573, - "rate":0.9970973177052372 - }, - "2":{ - "proportion":0.089878882017256, - "rate":3.244142488658602 + "omega":3.910413867333085, + "proportion":0.4584372725854091 } }, "Test":{ "0":{ "omega":0, - "proportion":0.3825895192221547 + "proportion":0.2968543549269862 }, "1":{ - "omega":0.9998114377116485, - "proportion":0 + "omega":0, + "proportion":0.2447083724876047 }, "2":{ - "omega":1.000029443594731, - "proportion":0.6174104807778453 + "omega":1.655264242043239, + "proportion":0.4584372725854091 } } }, "display order":2, - "estimated parameters":45 + "estimated parameters":36 }, "RELAX null":{ - "AIC-c":6919.152853316747, - "Log Likelihood":-3414.491495151524, + "AIC-c":6946.046147526199, + "Log Likelihood":-3437.336050862336, "Rate Distributions":{ "Reference":{ "0":{ - "omega":0, - "proportion":0.3885051761591228 + "omega":0.07516343499603452, + "proportion":0.2524283429126023 }, "1":{ - "omega":0.9958737025997172, - "proportion":0 + "omega":0.1730729265669467, + "proportion":0.3734402861071174 }, "2":{ - "omega":1.887643080900262, - "proportion":0.6114948238408772 - } - }, - "Synonymous site-to-site rates":{ - "0":{ - "proportion":0.2642938080646302, - "rate":0.2741590488311177 - }, - "1":{ - "proportion":0.633162055223991, - "rate":0.9728788992663913 - }, - "2":{ - "proportion":0.1025441367113787, - "rate":3.038218152856258 + "omega":3.70326279512502, + "proportion":0.3741313709802804 } }, "Test":{ "0":{ - "omega":0, - "proportion":0.3885051761591228 + "omega":0.07516343499603452, + "proportion":0.2524283429126023 }, "1":{ - "omega":0.9958737025997172, - "proportion":0 + "omega":0.1730729265669467, + "proportion":0.3734402861071174 }, "2":{ - "omega":1.887643080900262, - "proportion":0.6114948238408772 + "omega":3.70326279512502, + "proportion":0.3741313709802804 } } }, "display order":3, - "estimated parameters":44 + "estimated parameters":35 }, "RELAX partitioned descriptive":{ - "AIC-c":6917.810941882631, - "Log Likelihood":-3408.559317095162, + "AIC-c":6944.507313452719, + "Log Likelihood":-3431.356991882183, "Rate Distributions":{ "Reference":{ "0":{ - "omega":0.03550460650841439, - "proportion":0.354985198548996 + "omega":0, + "proportion":0.3694476627871225 }, "1":{ - "omega":0.05439939847728128, - "proportion":0.02231130867735708 + "omega":0.03660893085044142, + "proportion":0.1726741298596992 }, "2":{ - "omega":2.333762420535514, - "proportion":0.6227034927736469 + "omega":3.988980749944551, + "proportion":0.4578782073531784 } }, "Test":{ "0":{ - "omega":0, - "proportion":0.3705590531463396 + "omega":0.224878249826745, + "proportion":0.2953732524277409 }, "1":{ - "omega":0, - "proportion":0.06265340406614885 + "omega":0.231175241198686, + "proportion":0.5325206774143161 }, "2":{ - "omega":1.08372848194659, - "proportion":0.5667875427875115 + "omega":4.178788461910403, + "proportion":0.172106070157943 } } }, "display order":5, - "estimated parameters":49 + "estimated parameters":40 } }, "input":{ - "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex", + "file name":"/tmp/tmps1cqwvdh/job_working_directory/000/5/working/./input.nex", "number of sequences":10, "number of sites":187, "partition count":1, @@ -471,11 +438,11 @@ "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", + "runtime":"2.5.36", "test results":{ - "LRT":11.58431319646934, - "p-value":0.0006651049394417186, - "relaxation or intensification parameter":3.335337302186161e-05 + "LRT":9.706171521456781, + "p-value":0.001836502097725456, + "relaxation or intensification parameter":0.3695692925647034 }, "tested":{ "0":{ @@ -500,27 +467,27 @@ "timers":{ "General descriptive model fitting":{ "order":2, - "timer":105 + "timer":159 }, "Overall":{ "order":0, - "timer":3013 + "timer":428 }, "Preliminary model fitting":{ "order":1, - "timer":8 + "timer":13 }, "RELAX alternative model fitting":{ "order":3, - "timer":1229 + "timer":61 }, "RELAX null model fitting":{ "order":4, - "timer":690 + "timer":53 }, "RELAX partitioned descriptive":{ "order":5, - "timer":980 + "timer":141 } } } \ No newline at end of file