Mercurial > repos > iuc > hyphy_bgm

annotate test-data/relax-out1.json @ 25:d88bbb287923 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:01:09 +0000
parents bf97cacc1a55
children 5b6b8b08f1a9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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diff changeset
1 {
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d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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2 "analysis":0,
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3 "branch attributes":{
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4 "0":{
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5 "Baboon":{
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6 "General descriptive":0.001858767762813579,
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7 "MG94xREV with separate rates for branch sets":0.001769472024099301,
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8 "Nucleotide GTR":0.001680040630127455,
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9 "RELAX alternative":0.001872256662230973,
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11 "RELAX partitioned descriptive":0.001898170574782418,
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12 "k (general descriptive)":0.09971581394819819,
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13 "original name":"Baboon"
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14 },
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15 "Cat":{
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16 "General descriptive":0.3644803308678196,
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17 "MG94xREV with separate rates for branch sets":0.2796030091674721,
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18 "Nucleotide GTR":0.2660909938917123,
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19 "RELAX alternative":0.3689219388980864,
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22 "k (general descriptive)":2.314507643873676,
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23 "original name":"Cat"
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24 },
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25 "Chimp":{
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26 "General descriptive":0.001848680051431209,
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28 "Nucleotide GTR":0.001818373670119325,
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30 "RELAX null":0.00183525802483954,
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31 "RELAX partitioned descriptive":0.001832717232153088,
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33 "original name":"Chimp"
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34 },
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35 "Cow":{
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36 "General descriptive":0.3733627618450006,
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38 "Nucleotide GTR":0.2481025999892287,
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39 "RELAX alternative":0.342739998512865,
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40 "RELAX null":0.2948256709356563,
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41 "RELAX partitioned descriptive":0.3466331923230422,
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42 "k (general descriptive)":2.846155982935764,
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43 "original name":"Cow"
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44 },
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45 "Horse":{
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46 "General descriptive":0.2802176313870697,
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48 "Nucleotide GTR":0.2090310577070883,
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52 "k (general descriptive)":1.926646959057857,
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53 "original name":"Horse"
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54 },
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55 "Human":{
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56 "General descriptive":0,
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57 "MG94xREV with separate rates for branch sets":0,
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58 "Nucleotide GTR":0,
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59 "RELAX alternative":0,
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60 "RELAX null":0,
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62 "k (general descriptive)":1.462532487172471,
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63 "original name":"Human"
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64 },
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65 "Mouse":{
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68 "Nucleotide GTR":0.1180171198334285,
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73 "original name":"Mouse"
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75 "Node1":{
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76 "General descriptive":0.350050900813081,
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78 "Nucleotide GTR":0.2767237570684924,
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165 "MG94xREV with separate rates for branch sets":{
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166 "attribute type":"branch length",
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167 "display order":1
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168 },
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169 "Nucleotide GTR":{
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170 "attribute type":"branch length",
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171 "display order":0
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172 },
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173 "RELAX alternative":{
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174 "attribute type":"branch length",
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175 "display order":2
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176 },
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177 "RELAX null":{
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178 "attribute type":"branch length",
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179 "display order":3
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180 },
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181 "RELAX partitioned descriptive":{
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182 "attribute type":"branch length",
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183 "display order":5
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184 },
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185 "k (general descriptive)":{
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186 "attribute type":"branch label",
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187 "display order":4
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188 },
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189 "original name":{
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190 "attribute type":"node label",
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191 "display order":-1
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192 }
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193 }
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194 },
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195 "data partitions":{
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196 "0":{
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197 "coverage": [
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199 ],
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200 "name":"relax.filter.default"
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201 }
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202 },
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203 "fits":{
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204 "General descriptive":{
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diff changeset
205 "AIC-c":6945.891353881681,
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206 "Log Likelihood":-3420.486931066253,
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207 "Rate Distributions":{
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208 "Shared":{
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209 "0":{
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210 "omega":2.202835393423959e-18,
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211 "proportion":0.4487473029633234
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212 },
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213 "1":{
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214 "omega":2.202835393423959e-18,
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215 "proportion":0.09729227592412616
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216 },
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217 "2":{
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218 "omega":2.202835210940273,
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219 "proportion":0.4539604211125504
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220 }
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221 }
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222 },
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223 "display order":4,
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diff changeset
224 "estimated parameters":51
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225 },
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226 "MG94xREV with separate rates for branch sets":{
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227 "AIC-c":6987.565999172035,
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diff changeset
228 "Equilibrium frequencies": [
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289 [0.01189287130232129]
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290 ],
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291 "Log Likelihood":-3461.208149286616,
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292 "Rate Distributions":{
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293 "non-synonymous/synonymous rate ratio for *Reference*": [
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294 [0.7682335289209781, 1]
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295 ],
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296 "non-synonymous/synonymous rate ratio for *Test*": [
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297 [1.605439824256426, 1]
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298 ]
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299 },
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300 "display order":1,
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301 "estimated parameters":32
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302 },
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303 "Nucleotide GTR":{
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iuc
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304 "AIC-c":7112.857310169033,
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305 "Equilibrium frequencies": [
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306 [0.3592490842490842],
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309 [0.2187728937728937]
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310 ],
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311 "Log Likelihood":-3532.32122446679,
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312 "Rate Distributions":{
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313 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
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314 "Substitution rate from nucleotide A to nucleotide G":1,
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315 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
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316 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
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317 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
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318 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
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319 },
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320 "display order":0,
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321 "estimated parameters":24
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322 },
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323 "RELAX alternative":{
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324 "AIC-c":6931.922980697387,
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diff changeset
325 "Log Likelihood":-3429.234812770952,
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326 "Rate Distributions":{
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327 "Reference":{
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328 "0":{
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329 "omega":1.762268314739328e-19,
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diff changeset
330 "proportion":0.4504132080156107
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331 },
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diff changeset
332 "1":{
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diff changeset
333 "omega":1.762268314739328e-19,
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334 "proportion":0.08749553114962015
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335 },
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diff changeset
336 "2":{
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337 "omega":2.19971015101232,
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338 "proportion":0.4620912608347691
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339 }
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340 },
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341 "Test":{
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342 "0":{
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343 "omega":1.054840660215593e-44,
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344 "proportion":0.4504132080156107
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345 },
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346 "1":{
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347 "omega":1.054840660215593e-44,
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348 "proportion":0.08749553114962015
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349 },
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350 "2":{
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351 "omega":6.350765030542244,
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352 "proportion":0.4620912608347691
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353 }
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354 }
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355 },
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356 "display order":2,
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iuc
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357 "estimated parameters":36
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358 },
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359 "RELAX null":{
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360 "AIC-c":6946.046672507471,
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iuc
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361 "Log Likelihood":-3437.336313352972,
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362 "Rate Distributions":{
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363 "Reference":{
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364 "0":{
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365 "omega":0.1150006822953211,
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366 "proportion":0.542405144031307
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367 },
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368 "1":{
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369 "omega":0.2401508033814633,
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370 "proportion":0.08223353569636478
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371 },
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372 "2":{
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373 "omega":3.69263720947284,
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374 "proportion":0.3753613202723282
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375 }
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376 },
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377 "Test":{
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378 "0":{
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379 "omega":0.1150006822953211,
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380 "proportion":0.542405144031307
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381 },
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382 "1":{
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383 "omega":0.2401508033814633,
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384 "proportion":0.08223353569636478
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385 },
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386 "2":{
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387 "omega":3.69263720947284,
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388 "proportion":0.3753613202723282
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389 }
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390 }
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391 },
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392 "display order":3,
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iuc
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393 "estimated parameters":35
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394 },
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395 "RELAX partitioned descriptive":{
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396 "AIC-c":6937.04707353565,
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iuc
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397 "Log Likelihood":-3427.626871923648,
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398 "Rate Distributions":{
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399 "Reference":{
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400 "0":{
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401 "omega":0.1943306885168281,
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402 "proportion":0.3359458135547653
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403 },
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404 "1":{
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405 "omega":0.2607558478587815,
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406 "proportion":0.4332550437039296
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407 },
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408 "2":{
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409 "omega":4.134271224300374,
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410 "proportion":0.2307991427413052
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411 }
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412 },
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413 "Test":{
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414 "0":{
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415 "omega":0,
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416 "proportion":0.4753488415962343
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417 },
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418 "1":{
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419 "omega":0,
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420 "proportion":0.03858318603767072
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421 },
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422 "2":{
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423 "omega":6.017221959238516,
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iuc
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diff changeset
424 "proportion":0.486067972366095
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diff changeset
425 }
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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426 }
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427 },
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diff changeset
428 "display order":5,
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diff changeset
429 "estimated parameters":40
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430 }
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431 },
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diff changeset
432 "input":{
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diff changeset
433 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",
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434 "number of sequences":10,
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diff changeset
435 "number of sites":187,
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diff changeset
436 "partition count":1,
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diff changeset
437 "trees":{
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diff changeset
438 "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)"
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439 }
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440 },
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diff changeset
441 "test results":{
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diff changeset
442 "LRT":16.20300116404087,
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diff changeset
443 "p-value":5.690389451429301e-05,
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diff changeset
444 "relaxation or intensification parameter":2.344938789085876
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445 },
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diff changeset
446 "tested":{
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diff changeset
447 "0":{
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diff changeset
448 "Baboon":"Reference",
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diff changeset
449 "Cat":"Test",
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diff changeset
450 "Chimp":"Reference",
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diff changeset
451 "Cow":"Test",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
452 "Horse":"Test",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
453 "Human":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
454 "Mouse":"Reference",
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diff changeset
455 "Node1":"Reference",
d88bbb287923 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
456 "Node12":"Reference",
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diff changeset
457 "Node2":"Reference",
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diff changeset
458 "Node3":"Reference",
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diff changeset
459 "Node8":"Reference",
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diff changeset
460 "Node9":"Reference",
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diff changeset
461 "Pig":"Reference",
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diff changeset
462 "Rat":"Reference",
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iuc
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diff changeset
463 "RhMonkey":"Reference"
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464 }
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465 },
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diff changeset
466 "timers":{
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diff changeset
467 "General descriptive model fitting":{
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diff changeset
468 "order":2,
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diff changeset
469 "timer":132
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470 },
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diff changeset
471 "Overall":{
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472 "order":0,
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473 "timer":324
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474 },
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diff changeset
475 "Preliminary model fitting":{
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476 "order":1,
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477 "timer":8
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478 },
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diff changeset
479 "RELAX alternative model fitting":{
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diff changeset
480 "order":3,
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481 "timer":65
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482 },
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diff changeset
483 "RELAX null model fitting":{
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diff changeset
484 "order":4,
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485 "timer":66
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486 },
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diff changeset
487 "RELAX partitioned descriptive":{
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488 "order":5,
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489 "timer":53
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490 }
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492 }