Mercurial > repos > iuc > hyphy_prime
diff test-data/relax-out2-1.json @ 24:f207757f9ca2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
| author | iuc |
|---|---|
| date | Wed, 30 Mar 2022 00:20:28 +0000 |
| parents | 6d29207a32c5 |
| children | 0407236012e5 |
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--- a/test-data/relax-out2-1.json Sat Nov 27 11:34:27 2021 +0000 +++ b/test-data/relax-out2-1.json Wed Mar 30 00:20:28 2022 +0000 @@ -1,60 +1,60 @@ { "Synonymous site-posteriors": [ -[0.2717348381268465, 0.5635158143073038, 0.5580958985234344, 0.4419267392327456, 0.1775513314393873, 0.01303903284026798, 0.00125071980641974, 0.2376006215377312, 0.8837687913991302, 0.697488732253998, 0.76440666757549, 0.1859131352278527, 0.4676839084660329, 0.5320161033357819, 0.4513687349306337, 0.8514990846254493, 0.9101555767748879, 0.9112112654445478, 0.9624478616388369, 0.9472735837633918, 0.8715894173292342, 0.9248557783401865, 0.3852870058193366, 0.7504386709677574, 0.7275694213063354, 0.1979029930878776, 0.2585255313006612, 0.426812371619399, 0.03564414482172501, 0.3292941826787388, 0.1427864928730872, 0.8324822227281018, 0.9311167984186458, 0.1209539167468769, 0.8726642109588801, 1.798577785061191e-05, 0.584102863529593, 0.5747348035616634, 0.5814406651776627, 0.02251840852563282, 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+ "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