Mercurial > repos > iuc > hyphy_slac

comparison test-data/relax-out2-1.json @ 34:1467fb7e162d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author iuc
date Thu, 18 Aug 2022 13:56:28 +0000
parents 365e33adf3a4
children
comparison
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33:365e33adf3a4 34:1467fb7e162d
1 { 1 {
2 "Synonymous site-posteriors": [
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124 }, 119 },
125 "Node9":{ 120 "Node9":{
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134 "PIG":{ 129 "PIG":{
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136 "MG94xREV with separate rates for branch sets":0.1921302603267553, 131 "MG94xREV with separate rates for branch sets":0.1921302603267553,
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142 "original name":"PIG" 137 "original name":"PIG"
143 }, 138 },
144 "RAT":{ 139 "RAT":{
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146 "MG94xREV with separate rates for branch sets":0.06831927364558048, 141 "MG94xREV with separate rates for branch sets":0.06831927364558048,
147 "Nucleotide GTR":0.06661490534189227, 142 "Nucleotide GTR":0.06661490534189227,
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152 "original name":"RAT" 147 "original name":"RAT"
153 }, 148 },
154 "RHMONKEY":{ 149 "RHMONKEY":{
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156 "MG94xREV with separate rates for branch sets":0.003755247927570558, 151 "MG94xREV with separate rates for branch sets":0.003755247927570558,
157 "Nucleotide GTR":0.003778804730491441, 152 "Nucleotide GTR":0.003778804730491441,
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161 "k (general descriptive)":5.301456309232226, 156 "k (general descriptive)":5.244027200799457,
162 "original name":"RHMONKEY" 157 "original name":"RHMONKEY"
163 } 158 }
164 }, 159 },
165 "attributes":{ 160 "attributes":{
166 "General descriptive":{ 161 "General descriptive":{
205 "name":"relax.filter.default" 200 "name":"relax.filter.default"
206 } 201 }
207 }, 202 },
208 "fits":{ 203 "fits":{
209 "General descriptive":{ 204 "General descriptive":{
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211 "Log Likelihood":-3420.484282637879, 206 "Log Likelihood":-3420.484879880983,
212 "Rate Distributions":{ 207 "Rate Distributions":{
213 "Shared":{ 208 "Shared":{
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216 "proportion":0.5258178735075876 211 "proportion":0.1667516969215508
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222 "2":{ 217 "2":{
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225 } 220 }
226 } 221 }
227 }, 222 },
228 "display order":4, 223 "display order":4,
229 "estimated parameters":51 224 "estimated parameters":51
324 }, 319 },
325 "display order":0, 320 "display order":0,
326 "estimated parameters":24 321 "estimated parameters":24
327 }, 322 },
328 "RELAX alternative":{ 323 "RELAX alternative":{
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330 "Log Likelihood":-3408.69933855329, 325 "Log Likelihood":-3432.482965101608,
331 "Rate Distributions":{ 326 "Rate Distributions":{
332 "Reference":{ 327 "Reference":{
333 "0":{ 328 "0":{
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335 "proportion":0.3825895192221547 330 "proportion":0.2968543549269862
336 }, 331 },
337 "1":{ 332 "1":{
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344 }
345 },
346 "Synonymous site-to-site rates":{
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358 } 339 }
359 }, 340 },
360 "Test":{ 341 "Test":{
361 "0":{ 342 "0":{
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364 }, 345 },
365 "1":{ 346 "1":{
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368 }, 349 },
369 "2":{ 350 "2":{
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372 } 353 }
373 } 354 }
374 }, 355 },
375 "display order":2, 356 "display order":2,
376 "estimated parameters":45 357 "estimated parameters":36
377 }, 358 },
378 "RELAX null":{ 359 "RELAX null":{
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380 "Log Likelihood":-3414.491495151524, 361 "Log Likelihood":-3437.336050862336,
381 "Rate Distributions":{ 362 "Rate Distributions":{
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391 "2":{ 372 "2":{
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394 }
395 },
396 "Synonymous site-to-site rates":{
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399 "rate":0.2741590488311177
400 },
401 "1":{
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408 } 375 }
409 }, 376 },
410 "Test":{ 377 "Test":{
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380 "proportion":0.2524283429126023
381 },
382 "1":{
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389 }
390 }
391 },
392 "display order":3,
393 "estimated parameters":35
394 },
395 "RELAX partitioned descriptive":{
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397 "Log Likelihood":-3431.356991882183,
398 "Rate Distributions":{
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414 }, 403 },
415 "1":{ 404 "1":{
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419 "2":{ 408 "2":{
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422 }
423 }
424 },
425 "display order":3,
426 "estimated parameters":44
427 },
428 "RELAX partitioned descriptive":{
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430 "Log Likelihood":-3408.559317095162,
431 "Rate Distributions":{
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436 },
437 "1":{
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444 } 411 }
445 }, 412 },
446 "Test":{ 413 "Test":{
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449 "proportion":0.3705590531463396 416 "proportion":0.2953732524277409
450 }, 417 },
451 "1":{ 418 "1":{
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454 }, 421 },
455 "2":{ 422 "2":{
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458 } 425 }
459 } 426 }
460 }, 427 },
461 "display order":5, 428 "display order":5,
462 "estimated parameters":49 429 "estimated parameters":40
463 } 430 }
464 }, 431 },
465 "input":{ 432 "input":{
466 "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex", 433 "file name":"/tmp/tmps1cqwvdh/job_working_directory/000/5/working/./input.nex",
467 "number of sequences":10, 434 "number of sequences":10,
468 "number of sites":187, 435 "number of sites":187,
469 "partition count":1, 436 "partition count":1,
470 "trees":{ 437 "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)" 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)"
472 } 439 }
473 }, 440 },
474 "runtime":"2.5.32", 441 "runtime":"2.5.36",
475 "test results":{ 442 "test results":{
476 "LRT":11.58431319646934, 443 "LRT":9.706171521456781,
477 "p-value":0.0006651049394417186, 444 "p-value":0.001836502097725456,
478 "relaxation or intensification parameter":3.335337302186161e-05 445 "relaxation or intensification parameter":0.3695692925647034
479 }, 446 },
480 "tested":{ 447 "tested":{
481 "0":{ 448 "0":{
482 "BABOON":"Test", 449 "BABOON":"Test",
483 "CAT":"Reference", 450 "CAT":"Reference",
498 } 465 }
499 }, 466 },
500 "timers":{ 467 "timers":{
501 "General descriptive model fitting":{ 468 "General descriptive model fitting":{
502 "order":2, 469 "order":2,
503 "timer":105 470 "timer":159
504 }, 471 },
505 "Overall":{ 472 "Overall":{
506 "order":0, 473 "order":0,
507 "timer":3013 474 "timer":428
508 }, 475 },
509 "Preliminary model fitting":{ 476 "Preliminary model fitting":{
510 "order":1, 477 "order":1,
511 "timer":8 478 "timer":13
512 }, 479 },
513 "RELAX alternative model fitting":{ 480 "RELAX alternative model fitting":{
514 "order":3, 481 "order":3,
515 "timer":1229 482 "timer":61
516 }, 483 },
517 "RELAX null model fitting":{ 484 "RELAX null model fitting":{
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519 "timer":690 486 "timer":53
520 }, 487 },
521 "RELAX partitioned descriptive":{ 488 "RELAX partitioned descriptive":{
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523 "timer":980 490 "timer":141
524 } 491 }
525 } 492 }
526 } 493 }