Mercurial > repos > iuc > hyphy_fade

comparison test-data/relax-out2-1.json @ 32:eb23ebaf69d2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:14:22 +0000
parents 5e8d0e777033
children a73fff151e38
comparison
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31:ac0dea1caeab 32:eb23ebaf69d2
1 { 1 {
2 "Synonymous site-posteriors": [ 2 "Synonymous site-posteriors": [
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140 "RELAX partitioned descriptive":0.251294309938668, 140 "RELAX partitioned descriptive":0.2506475053874151,
141 "k (general descriptive)":1.57905583202459, 141 "k (general descriptive)":1.582105640200874,
142 "original name":"PIG" 142 "original name":"PIG"
143 }, 143 },
144 "RAT":{ 144 "RAT":{
145 "General descriptive":0.07161013387643886, 145 "General descriptive":0.07158272879959397,
146 "MG94xREV with separate rates for branch sets":0.06830746072347418, 146 "MG94xREV with separate rates for branch sets":0.06831927364558048,
147 "Nucleotide GTR":0.06661283005976348, 147 "Nucleotide GTR":0.06661490534189227,
148 "RELAX alternative":0.07293805936494982, 148 "RELAX alternative":0.07311180317129368,
149 "RELAX null":0.07115038941652747, 149 "RELAX null":0.07112698282214641,
150 "RELAX partitioned descriptive":0.07467247582140474, 150 "RELAX partitioned descriptive":0.07451416024404128,
151 "k (general descriptive)":1.319839560623237, 151 "k (general descriptive)":1.317928928374736,
152 "original name":"RAT" 152 "original name":"RAT"
153 }, 153 },
154 "RHMONKEY":{ 154 "RHMONKEY":{
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156 "MG94xREV with separate rates for branch sets":0.003753885794232333, 156 "MG94xREV with separate rates for branch sets":0.003755247927570558,
157 "Nucleotide GTR":0.003775170135617877, 157 "Nucleotide GTR":0.003778804730491441,
158 "RELAX alternative":0.004180662465434332, 158 "RELAX alternative":0.004176749981889291,
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161 "k (general descriptive)":5.183560186695944, 161 "k (general descriptive)":5.301456309232226,
162 "original name":"RHMONKEY" 162 "original name":"RHMONKEY"
163 } 163 }
164 }, 164 },
165 "attributes":{ 165 "attributes":{
166 "General descriptive":{ 166 "General descriptive":{
205 "name":"relax.filter.default" 205 "name":"relax.filter.default"
206 } 206 }
207 }, 207 },
208 "fits":{ 208 "fits":{
209 "General descriptive":{ 209 "General descriptive":{
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211 "Log Likelihood":-3420.486789501042, 211 "Log Likelihood":-3420.484282637879,
212 "Rate Distributions":{ 212 "Rate Distributions":{
213 "Shared":{ 213 "Shared":{
214 "0":{ 214 "0":{
215 "omega":2.20271427504516e-18, 215 "omega":2.201373594751134e-18,
216 "proportion":0.00789425874100967 216 "proportion":0.5258178735075876
217 }, 217 },
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220 "proportion":0.5381203586928067 220 "proportion":0.01992025780064184
221 }, 221 },
222 "2":{ 222 "2":{
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225 } 225 }
226 } 226 }
227 }, 227 },
228 "display order":4, 228 "display order":4,
229 "estimated parameters":51 229 "estimated parameters":51
230 }, 230 },
231 "MG94xREV with separate rates for branch sets":{ 231 "MG94xREV with separate rates for branch sets":{
232 "AIC-c":6987.278662183248, 232 "AIC-c":6987.278076404838,
233 "Equilibrium frequencies": [ 233 "Equilibrium frequencies": [
234 [0.04876086397632926], 234 [0.04876086397632926],
235 [0.03982224127745371], 235 [0.03982224127745371],
236 [0.0494959405650269], 236 [0.0494959405650269],
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291 [0.01396413011303752], 291 [0.01396413011303752],
292 [0.01140428846505027], 292 [0.01140428846505027],
293 [0.01417464125436193], 293 [0.01417464125436193],
294 [0.01189287130232129] 294 [0.01189287130232129]
295 ], 295 ],
296 "Log Likelihood":-3461.064480792223, 296 "Log Likelihood":-3461.064187903018,
297 "Rate Distributions":{ 297 "Rate Distributions":{
298 "non-synonymous/synonymous rate ratio for *Reference*": [ 298 "non-synonymous/synonymous rate ratio for *Reference*": [
299 [1.240656122625563, 1] 299 [1.243401858007084, 1]
300 ], 300 ],
301 "non-synonymous/synonymous rate ratio for *Test*": [ 301 "non-synonymous/synonymous rate ratio for *Test*": [
302 [0.5611761689874598, 1] 302 [0.5612874934764923, 1]
303 ] 303 ]
304 }, 304 },
305 "display order":1, 305 "display order":1,
306 "estimated parameters":32 306 "estimated parameters":32
307 }, 307 },
308 "Nucleotide GTR":{ 308 "Nucleotide GTR":{
309 "AIC-c":7112.857310169033, 309 "AIC-c":7112.857288723968,
310 "Equilibrium frequencies": [ 310 "Equilibrium frequencies": [
311 [0.3592490842490842], 311 [0.3592490842490842],
312 [0.181959706959707], 312 [0.181959706959707],
313 [0.240018315018315], 313 [0.240018315018315],
314 [0.2187728937728937] 314 [0.2187728937728937]
315 ], 315 ],
316 "Log Likelihood":-3532.32122446679, 316 "Log Likelihood":-3532.321213744258,
317 "Rate Distributions":{ 317 "Rate Distributions":{
318 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087, 318 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
319 "Substitution rate from nucleotide A to nucleotide G":1, 319 "Substitution rate from nucleotide A to nucleotide G":1,
320 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847, 320 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
321 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032, 321 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
322 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795, 322 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
323 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575 323 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
324 }, 324 },
325 "display order":0, 325 "display order":0,
326 "estimated parameters":24 326 "estimated parameters":24
327 }, 327 },
328 "RELAX alternative":{ 328 "RELAX alternative":{
329 "AIC-c":6901.392449196474, 329 "AIC-c":6909.668413948684,
330 "Log Likelihood":-3408.754211469135, 330 "Log Likelihood":-3408.69933855329,
331 "Rate Distributions":{ 331 "Rate Distributions":{
332 "Reference":{ 332 "Reference":{
333 "0":{ 333 "0":{
334 "omega":0, 334 "omega":0,
335 "proportion":0.3814061972635792 335 "proportion":0.3825895192221547
336 }, 336 },
337 "1":{ 337 "1":{
338 "omega":0.4330262245823013, 338 "omega":0.003503464580598538,
339 "proportion":0 339 "proportion":0
340 }, 340 },
341 "2":{ 341 "2":{
342 "omega":2.405594515133199, 342 "omega":2.417572962231385,
343 "proportion":0.6185938027364208 343 "proportion":0.6174104807778453
344 } 344 }
345 }, 345 },
346 "Synonymous site-to-site rates":{ 346 "Synonymous site-to-site rates":{
347 "0":{ 347 "0":{
348 "proportion":0.2800901562602482, 348 "proportion":0.2789425737851868,
349 "rate":0.2837970682663188 349 "rate":0.2834765074731829
350 }, 350 },
351 "1":{ 351 "1":{
352 "proportion":0.6272754947629234, 352 "proportion":0.6311785441975573,
353 "rate":0.9947075941569237 353 "rate":0.9970973177052372
354 }, 354 },
355 "2":{ 355 "2":{
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357 "rate":3.20135608237551 357 "rate":3.244142488658602
358 } 358 }
359 }, 359 },
360 "Test":{ 360 "Test":{
361 "0":{ 361 "0":{
362 "omega":0, 362 "omega":0,
363 "proportion":0.3814061972635792 363 "proportion":0.3825895192221547
364 }, 364 },
365 "1":{ 365 "1":{
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367 "proportion":0 367 "proportion":0
368 }, 368 },
369 "2":{ 369 "2":{
370 "omega":1.00002621592498, 370 "omega":1.000029443594731,
371 "proportion":0.6185938027364208 371 "proportion":0.6174104807778453
372 } 372 }
373 } 373 }
374 }, 374 },
375 "display order":2, 375 "display order":2,
376 "estimated parameters":41 376 "estimated parameters":45
377 }, 377 },
378 "RELAX null":{ 378 "RELAX null":{
379 "AIC-c":6910.777215627525, 379 "AIC-c":6919.152853316747,
380 "Log Likelihood":-3414.491942969586, 380 "Log Likelihood":-3414.491495151524,
381 "Rate Distributions":{ 381 "Rate Distributions":{
382 "Reference":{ 382 "Reference":{
383 "0":{ 383 "0":{
384 "omega":0, 384 "omega":0,
385 "proportion":0.04600287725570656 385 "proportion":0.3885051761591228
386 }, 386 },
387 "1":{ 387 "1":{
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390 }, 390 },
391 "2":{ 391 "2":{
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393 "proportion":0.6107504463948045 393 "proportion":0.6114948238408772
394 } 394 }
395 }, 395 },
396 "Synonymous site-to-site rates":{ 396 "Synonymous site-to-site rates":{
397 "0":{ 397 "0":{
398 "proportion":0.2641095265325168, 398 "proportion":0.2642938080646302,
399 "rate":0.2744837794048847 399 "rate":0.2741590488311177
400 }, 400 },
401 "1":{ 401 "1":{
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407 "rate":3.029415427453047 407 "rate":3.038218152856258
408 } 408 }
409 }, 409 },
410 "Test":{ 410 "Test":{
411 "0":{ 411 "0":{
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413 "proportion":0.04600287725570656 413 "proportion":0.3885051761591228
414 }, 414 },
415 "1":{ 415 "1":{
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419 "2":{ 419 "2":{
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421 "proportion":0.6107504463948045 421 "proportion":0.6114948238408772
422 } 422 }
423 } 423 }
424 }, 424 },
425 "display order":3, 425 "display order":3,
426 "estimated parameters":40 426 "estimated parameters":44
427 }, 427 },
428 "RELAX partitioned descriptive":{ 428 "RELAX partitioned descriptive":{
429 "AIC-c":6909.42794543134, 429 "AIC-c":6917.810941882631,
430 "Log Likelihood":-3408.579104294618, 430 "Log Likelihood":-3408.559317095162,
431 "Rate Distributions":{ 431 "Rate Distributions":{
432 "Reference":{ 432 "Reference":{
433 "0":{ 433 "0":{
434 "omega":0.05035684771569529, 434 "omega":0.03550460650841439,
435 "proportion":0.3805224005150026 435 "proportion":0.354985198548996
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437 "1":{ 437 "1":{
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439 "proportion":0.003462124163764896 439 "proportion":0.02231130867735708
440 }, 440 },
441 "2":{ 441 "2":{
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443 "proportion":0.6160154753212325 443 "proportion":0.6227034927736469
444 } 444 }
445 }, 445 },
446 "Test":{ 446 "Test":{
447 "0":{ 447 "0":{
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449 "proportion":0.03160127773820932 449 "proportion":0.3705590531463396
450 }, 450 },
451 "1":{ 451 "1":{
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453 "proportion":0.4079248249859382 453 "proportion":0.06265340406614885
454 }, 454 },
455 "2":{ 455 "2":{
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457 "proportion":0.5604738972758525 457 "proportion":0.5667875427875115
458 } 458 }
459 } 459 }
460 }, 460 },
461 "display order":5, 461 "display order":5,
462 "estimated parameters":45 462 "estimated parameters":49
463 } 463 }
464 }, 464 },
465 "input":{ 465 "input":{
466 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/5/working/./input.nex", 466 "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex",
467 "number of sequences":10, 467 "number of sequences":10,
468 "number of sites":187, 468 "number of sites":187,
469 "partition count":1, 469 "partition count":1,
470 "trees":{ 470 "trees":{
471 "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)" 471 "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)"
472 } 472 }
473 }, 473 },
474 "runtime":"2.5.32",
474 "test results":{ 475 "test results":{
475 "LRT":11.47546300090198, 476 "LRT":11.58431319646934,
476 "p-value":0.0007052107640865835, 477 "p-value":0.0006651049394417186,
477 "relaxation or intensification parameter":2.986519568748539e-05 478 "relaxation or intensification parameter":3.335337302186161e-05
478 }, 479 },
479 "tested":{ 480 "tested":{
480 "0":{ 481 "0":{
481 "BABOON":"Test", 482 "BABOON":"Test",
482 "CAT":"Reference", 483 "CAT":"Reference",
497 } 498 }
498 }, 499 },
499 "timers":{ 500 "timers":{
500 "General descriptive model fitting":{ 501 "General descriptive model fitting":{
501 "order":2, 502 "order":2,
502 "timer":127 503 "timer":105
503 }, 504 },
504 "Overall":{ 505 "Overall":{
505 "order":0, 506 "order":0,
506 "timer":645 507 "timer":3013
507 }, 508 },
508 "Preliminary model fitting":{ 509 "Preliminary model fitting":{
509 "order":1, 510 "order":1,
510 "timer":8 511 "timer":8
511 }, 512 },
512 "RELAX alternative model fitting":{ 513 "RELAX alternative model fitting":{
513 "order":3, 514 "order":3,
514 "timer":178 515 "timer":1229
515 }, 516 },
516 "RELAX null model fitting":{ 517 "RELAX null model fitting":{
517 "order":4, 518 "order":4,
518 "timer":115 519 "timer":690
519 }, 520 },
520 "RELAX partitioned descriptive":{ 521 "RELAX partitioned descriptive":{
521 "order":5, 522 "order":5,
522 "timer":216 523 "timer":980
523 } 524 }
524 } 525 }
525 } 526 }