Mercurial > repos > iuc > hyphy_sm19

comparison test-data/relax-out1.json @ 32:00b4cf477625 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 00:22:46 +0000
parents 36e40d93e8a3
children
comparison
equal deleted inserted replaced
31:1527f00ddf7f 32:00b4cf477625
1 { 1 {
2 "analysis":0, 2 "analysis":0,
3 "branch attributes":{ 3 "branch attributes":{
4 "0":{ 4 "0":{
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8 "Nucleotide GTR":0.001680040630127455, 8 "Nucleotide GTR":0.001685167654714891,
9 "RELAX alternative":0.001872256662230973, 9 "RELAX alternative":0.001873708670384941,
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13 "original name":"Baboon" 13 "original name":"Baboon"
14 }, 14 },
15 "Cat":{ 15 "Cat":{
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23 "original name":"Cat" 23 "original name":"Cat"
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34 }, 34 },
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54 }, 54 },
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63 "original name":"Human" 63 "original name":"Human"
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120 "Node9":{ 120 "Node9":{
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137 "original name":"Pig" 137 "original name":"Pig"
138 }, 138 },
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147 "original name":"Rat" 147 "original name":"Rat"
148 }, 148 },
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157 "original name":"RhMonkey" 157 "original name":"RhMonkey"
158 } 158 }
159 }, 159 },
160 "attributes":{ 160 "attributes":{
161 "General descriptive":{ 161 "General descriptive":{
200 "name":"relax.filter.default" 200 "name":"relax.filter.default"
201 } 201 }
202 }, 202 },
203 "fits":{ 203 "fits":{
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207 "Rate Distributions":{ 207 "Rate Distributions":{
208 "Shared":{ 208 "Shared":{
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220 } 220 }
221 } 221 }
222 }, 222 },
223 "display order":4, 223 "display order":4,
224 "estimated parameters":51 224 "estimated parameters":51
225 }, 225 },
226 "MG94xREV with separate rates for branch sets":{ 226 "MG94xREV with separate rates for branch sets":{
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228 "Equilibrium frequencies": [ 228 "Equilibrium frequencies": [
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230 [0.03982224127745371], 230 [0.03982224127745371],
231 [0.0494959405650269], 231 [0.0494959405650269],
232 [0.04152830682371345], 232 [0.04152830682371345],
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288 [0.01417464125436193], 288 [0.01417464125436193],
289 [0.01189287130232129] 289 [0.01189287130232129]
290 ], 290 ],
291 "Log Likelihood":-3461.208149286616, 291 "Log Likelihood":-3461.208406480981,
292 "Rate Distributions":{ 292 "Rate Distributions":{
293 "non-synonymous/synonymous rate ratio for *Reference*": [ 293 "non-synonymous/synonymous rate ratio for *Reference*": [
294 [0.7682335289209781, 1] 294 [0.7685912547191639, 1]
295 ], 295 ],
296 "non-synonymous/synonymous rate ratio for *Test*": [ 296 "non-synonymous/synonymous rate ratio for *Test*": [
297 [1.605439824256426, 1] 297 [1.603198088111489, 1]
298 ] 298 ]
299 }, 299 },
300 "display order":1, 300 "display order":1,
301 "estimated parameters":32 301 "estimated parameters":32
302 }, 302 },
303 "Nucleotide GTR":{ 303 "Nucleotide GTR":{
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305 "Equilibrium frequencies": [ 305 "Equilibrium frequencies": [
306 [0.3592490842490842], 306 [0.3592490842490842],
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308 [0.240018315018315], 308 [0.240018315018315],
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310 ], 310 ],
311 "Log Likelihood":-3532.32122446679, 311 "Log Likelihood":-3532.321213744258,
312 "Rate Distributions":{ 312 "Rate Distributions":{
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314 "Substitution rate from nucleotide A to nucleotide G":1, 314 "Substitution rate from nucleotide A to nucleotide G":1,
315 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847, 315 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
316 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032, 316 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
317 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795, 317 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
318 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575 318 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
319 }, 319 },
320 "display order":0, 320 "display order":0,
321 "estimated parameters":24 321 "estimated parameters":24
322 }, 322 },
323 "RELAX alternative":{ 323 "RELAX alternative":{
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339 } 339 }
340 }, 340 },
341 "Test":{ 341 "Test":{
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355 }, 355 },
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358 }, 358 },
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376 }, 376 },
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390 } 390 }
391 }, 391 },
392 "display order":3, 392 "display order":3,
393 "estimated parameters":35 393 "estimated parameters":35
394 }, 394 },
395 "RELAX partitioned descriptive":{ 395 "RELAX partitioned descriptive":{
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398 "Rate Distributions":{ 398 "Rate Distributions":{
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428 "display order":5, 428 "display order":5,
429 "estimated parameters":40 429 "estimated parameters":40
430 } 430 }
431 }, 431 },
432 "input":{ 432 "input":{
433 "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta", 433 "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",
434 "number of sequences":10, 434 "number of sequences":10,
435 "number of sites":187, 435 "number of sites":187,
436 "partition count":1, 436 "partition count":1,
437 "trees":{ 437 "trees":{
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)" 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)"
439 } 439 }
440 }, 440 },
441 "runtime":"2.5.32",
441 "test results":{ 442 "test results":{
442 "LRT":16.20300116404087, 443 "LRT":16.80113246476958,
443 "p-value":5.690389451429301e-05, 444 "p-value":4.150852429507523e-05,
444 "relaxation or intensification parameter":2.344938789085876 445 "relaxation or intensification parameter":2.334214628944839
445 }, 446 },
446 "tested":{ 447 "tested":{
447 "0":{ 448 "0":{
448 "Baboon":"Reference", 449 "Baboon":"Reference",
449 "Cat":"Test", 450 "Cat":"Test",
464 } 465 }
465 }, 466 },
466 "timers":{ 467 "timers":{
467 "General descriptive model fitting":{ 468 "General descriptive model fitting":{
468 "order":2, 469 "order":2,
469 "timer":132 470 "timer":127
470 }, 471 },
471 "Overall":{ 472 "Overall":{
472 "order":0, 473 "order":0,
473 "timer":324 474 "timer":396
474 }, 475 },
475 "Preliminary model fitting":{ 476 "Preliminary model fitting":{
476 "order":1, 477 "order":1,
477 "timer":8 478 "timer":8
478 }, 479 },
479 "RELAX alternative model fitting":{ 480 "RELAX alternative model fitting":{
480 "order":3, 481 "order":3,
481 "timer":65 482 "timer":103
482 }, 483 },
483 "RELAX null model fitting":{ 484 "RELAX null model fitting":{
484 "order":4, 485 "order":4,
485 "timer":66 486 "timer":41
486 }, 487 },
487 "RELAX partitioned descriptive":{ 488 "RELAX partitioned descriptive":{
488 "order":5, 489 "order":5,
489 "timer":53 490 "timer":116
490 } 491 }
491 } 492 }
492 } 493 }