Mercurial > repos > iuc > hyphy_conv

annotate test-data/relax-out1.json @ 11:beeeed9665ea draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:10:54 +0000
parents 3ea647006f17
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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1 {
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2 "analysis":0,
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139 "Rat":{
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142 "Nucleotide GTR":0.06661490534189227,
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iuc
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diff changeset
152 "Nucleotide GTR":0.003778804730491441,
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diff changeset
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diff changeset
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diff changeset
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160 "attributes":{
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diff changeset
162 "attribute type":"branch length",
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diff changeset
169 "Nucleotide GTR":{
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diff changeset
170 "attribute type":"branch length",
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171 "display order":0
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diff changeset
172 },
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diff changeset
173 "RELAX alternative":{
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diff changeset
174 "attribute type":"branch length",
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diff changeset
175 "display order":2
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diff changeset
176 },
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diff changeset
177 "RELAX null":{
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diff changeset
178 "attribute type":"branch length",
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diff changeset
179 "display order":3
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diff changeset
180 },
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181 "RELAX partitioned descriptive":{
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diff changeset
182 "attribute type":"branch length",
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diff changeset
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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diff changeset
189 "original name":{
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190 "attribute type":"node label",
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191 "display order":-1
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diff changeset
192 }
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193 }
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diff changeset
195 "data partitions":{
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196 "0":{
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diff changeset
197 "coverage": [
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diff changeset
198 [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]
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diff changeset
199 ],
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diff changeset
200 "name":"relax.filter.default"
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diff changeset
201 }
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202 },
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diff changeset
203 "fits":{
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diff changeset
204 "General descriptive":{
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diff changeset
205 "AIC-c":6945.892677835464,
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diff changeset
206 "Log Likelihood":-3420.487593043145,
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diff changeset
207 "Rate Distributions":{
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diff changeset
208 "Shared":{
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diff changeset
209 "0":{
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diff changeset
210 "omega":2.201451464048879e-18,
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diff changeset
211 "proportion":0.3073650505039141
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212 },
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diff changeset
213 "1":{
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diff changeset
214 "omega":2.201451464048879e-18,
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diff changeset
215 "proportion":0.2383891488636319
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216 },
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diff changeset
217 "2":{
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diff changeset
218 "omega":2.201451281679838,
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diff changeset
219 "proportion":0.4542458006324541
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220 }
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diff changeset
221 }
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222 },
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diff changeset
223 "display order":4,
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diff changeset
224 "estimated parameters":51
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diff changeset
225 },
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diff changeset
226 "MG94xREV with separate rates for branch sets":{
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diff changeset
227 "AIC-c":6987.566513560764,
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diff changeset
228 "Equilibrium frequencies": [
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229 [0.04876086397632926],
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290 ],
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291 "Log Likelihood":-3461.208406480981,
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292 "Rate Distributions":{
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293 "non-synonymous/synonymous rate ratio for *Reference*": [
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294 [0.7685912547191639, 1]
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296 "non-synonymous/synonymous rate ratio for *Test*": [
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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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304 "AIC-c":7112.857288723968,
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305 "Equilibrium frequencies": [
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310 ],
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311 "Log Likelihood":-3532.321213744258,
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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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diff changeset
315 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
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diff changeset
316 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
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317 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
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diff changeset
318 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
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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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diff changeset
324 "AIC-c":6931.926773483473,
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diff changeset
325 "Log Likelihood":-3429.236709163995,
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326 "Rate Distributions":{
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327 "Reference":{
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328 "0":{
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diff changeset
329 "omega":1.761161171239182e-19,
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diff changeset
330 "proportion":0.2691773911207853
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diff changeset
331 },
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diff changeset
332 "1":{
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diff changeset
333 "omega":1.762922332410267e-19,
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diff changeset
334 "proportion":0.2692122656891806
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335 },
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diff changeset
336 "2":{
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diff changeset
337 "omega":2.208286837998088,
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diff changeset
338 "proportion":0.4616103431900341
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diff changeset
339 }
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340 },
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341 "Test":{
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343 "omega":1.673670300056362e-44,
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344 "proportion":0.2691773911207853
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345 },
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346 "1":{
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347 "omega":1.677579612236672e-44,
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348 "proportion":0.2692122656891806
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349 },
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350 "2":{
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351 "omega":6.354762788556926,
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352 "proportion":0.4616103431900341
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354 }
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355 },
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356 "display order":2,
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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":6946.648596594286,
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diff changeset
361 "Log Likelihood":-3437.63727539638,
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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":1.408928936991542e-20,
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366 "proportion":0.265244047162938
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368 "1":{
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370 "proportion":0.28512630848952
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372 "2":{
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373 "omega":3.213510017765925,
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374 "proportion":0.4496296443475419
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376 },
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377 "Test":{
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379 "omega":1.408928936991542e-20,
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380 "proportion":0.265244047162938
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381 },
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382 "1":{
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383 "omega":1.410337865928411e-20,
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384 "proportion":0.28512630848952
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385 },
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386 "2":{
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387 "omega":3.213510017765925,
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388 "proportion":0.4496296443475419
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389 }
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390 }
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391 },
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diff changeset
392 "display order":3,
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iuc
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diff changeset
393 "estimated parameters":35
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394 },
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395 "RELAX partitioned descriptive":{
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diff changeset
396 "AIC-c":6937.049237937651,
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iuc
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diff changeset
397 "Log Likelihood":-3427.627954124649,
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diff changeset
398 "Rate Distributions":{
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399 "Reference":{
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400 "0":{
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401 "omega":0.1847557016619168,
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diff changeset
402 "proportion":0.4766160247339328
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403 },
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404 "1":{
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diff changeset
405 "omega":0.3367540359539261,
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diff changeset
406 "proportion":0.3005513276312735
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407 },
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408 "2":{
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diff changeset
409 "omega":4.272816072857538,
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diff changeset
410 "proportion":0.2228326476347937
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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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diff changeset
415 "omega":1.127143149593234e-21,
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diff changeset
416 "proportion":0.2367540589657237
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417 },
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418 "1":{
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diff changeset
419 "omega":1.128270292740756e-21,
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diff changeset
420 "proportion":0.2771164325302933
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421 },
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422 "2":{
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diff changeset
423 "omega":6.023626417874829,
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diff changeset
424 "proportion":0.4861295085039831
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diff changeset
425 }
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iuc
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diff changeset
426 }
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iuc
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diff changeset
427 },
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iuc
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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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diff changeset
431 },
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diff changeset
432 "input":{
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diff changeset
433 "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",
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diff changeset
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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diff changeset
439 }
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diff changeset
440 },
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diff changeset
441 "runtime":"2.5.32",
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iuc
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diff changeset
442 "test results":{
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iuc
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diff changeset
443 "LRT":16.80113246476958,
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iuc
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diff changeset
444 "p-value":4.150852429507523e-05,
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iuc
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diff changeset
445 "relaxation or intensification parameter":2.334214628944839
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diff changeset
446 },
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diff changeset
447 "tested":{
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diff changeset
448 "0":{
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iuc
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diff changeset
449 "Baboon":"Reference",
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iuc
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diff changeset
450 "Cat":"Test",
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diff changeset
451 "Chimp":"Reference",
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iuc
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diff changeset
452 "Cow":"Test",
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iuc
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diff changeset
453 "Horse":"Test",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
454 "Human":"Reference",
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iuc
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diff changeset
455 "Mouse":"Reference",
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iuc
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diff changeset
456 "Node1":"Reference",
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iuc
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diff changeset
457 "Node12":"Reference",
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iuc
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diff changeset
458 "Node2":"Reference",
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iuc
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diff changeset
459 "Node3":"Reference",
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iuc
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diff changeset
460 "Node8":"Reference",
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iuc
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diff changeset
461 "Node9":"Reference",
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iuc
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diff changeset
462 "Pig":"Reference",
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iuc
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diff changeset
463 "Rat":"Reference",
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iuc
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diff changeset
464 "RhMonkey":"Reference"
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iuc
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diff changeset
465 }
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iuc
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diff changeset
466 },
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iuc
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diff changeset
467 "timers":{
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diff changeset
468 "General descriptive model fitting":{
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diff changeset
469 "order":2,
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3ea647006f17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
470 "timer":127
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diff changeset
471 },
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diff changeset
472 "Overall":{
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diff changeset
473 "order":0,
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diff changeset
474 "timer":396
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diff changeset
475 },
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diff changeset
476 "Preliminary model fitting":{
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diff changeset
477 "order":1,
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diff changeset
478 "timer":8
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diff changeset
479 },
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diff changeset
480 "RELAX alternative model fitting":{
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diff changeset
481 "order":3,
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482 "timer":103
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diff changeset
483 },
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diff changeset
484 "RELAX null model fitting":{
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diff changeset
485 "order":4,
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diff changeset
486 "timer":41
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diff changeset
487 },
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diff changeset
488 "RELAX partitioned descriptive":{
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diff changeset
489 "order":5,
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490 "timer":116
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diff changeset
491 }
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492 }
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493 }