Mercurial > repos > iuc > hyphy_relax

comparison test-data/summary/nsp8.RELAX.json @ 26:6d89dc242c2a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:02:18 +0000
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25:a4c5dc437558 26:6d89dc242c2a
1 {
2 "Synonymous site-posteriors": [
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168 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
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175 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
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182 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
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189 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
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195 },
196 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":{
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201 "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human"
202 },
203 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{
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208 "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human"
209 },
210 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
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216 },
217 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
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223 },
224 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
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230 },
231 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
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236 "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human"
237 },
238 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
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240 "Nucleotide GTR":0.003374190741831846,
241 "RELAX alternative":0.003507645115982479,
242 "RELAX null":0.003508905377887805,
243 "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human"
244 },
245 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
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248 "RELAX alternative":0.003504702597413055,
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250 "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human"
251 }
252 },
253 "attributes":{
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258 "Nucleotide GTR":{
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262 "RELAX alternative":{
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266 "RELAX null":{
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269 },
270 "original name":{
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273 }
274 }
275 },
276 "data partitions":{
277 "0":{
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280 ],
281 "name":"relax.filter.default"
282 }
283 },
284 "fits":{
285 "MG94xREV with separate rates for branch sets":{
286 "AIC-c":2512.992528250552,
287 "Equilibrium frequencies": [
288 [0.03825952761243274],
289 [0.01370948533169502],
290 [0.0238326285579188],
291 [0.05169206288834598],
292 [0.02910782227384961],
293 [0.01043016700423795],
294 [0.01813184740308045],
295 [0.03932728586627101],
296 [0.01035067712195123],
297 [0.003708944282165923],
298 [0.006447644771501305],
299 [0.01398469573761802],
300 [0.0283653688047424],
301 [0.01016412464618009],
302 [0.01766935821790241],
303 [0.03832416445281453],
304 [0.01521889661505549],
305 [0.005453366858635389],
306 [0.009480156518454269],
307 [0.02056209812326697],
308 [0.01157852606970437],
309 [0.004148917752546374],
310 [0.007212496554133422],
311 [0.01564363009947405],
312 [0.00411729822204095],
313 [0.001475345962268018],
314 [0.002564747797779777],
315 [0.005562840210150803],
316 [0.01128319250724396],
317 [0.004043091272315801],
318 [0.007028527343480687],
319 [0.01524460789411934],
320 [0.03592403244011121],
321 [0.01287261047188149],
322 [0.02237780168434643],
323 [0.04853659885475865],
324 [0.02733097915424774],
325 [0.009793473186905268],
326 [0.01702501611901085],
327 [0.03692661100139533],
328 [0.009718835644621534],
329 [0.003482537371104292],
330 [0.0060540580187001],
331 [0.01313102107355921],
332 [0.02663384763763138],
333 [0.009543670983435077],
334 [0.01659075888876379],
335 [0.0359847236220365],
336 [0.00848480075962617],
337 [0.03199221880690793],
338 [0.01801483181642438],
339 [0.006455230577911434],
340 [0.01122180073845716],
341 [0.02433965804833868],
342 [0.002295465694104339],
343 [0.003990447484454917],
344 [0.008655128485630147],
345 [0.01755532734880559],
346 [0.00629057695692368],
347 [0.01093556617204019],
348 [0.02371882618448924]
349 ],
350 "Log Likelihood":-1204.057620165384,
351 "Rate Distributions":{
352 "non-synonymous/synonymous rate ratio for *Reference*": [
353 [0, 1]
354 ],
355 "non-synonymous/synonymous rate ratio for *Test*": [
356 [21.18256670135096, 1]
357 ],
358 "non-synonymous/synonymous rate ratio for *Unclassified*": [
359 [0.5156677179593993, 1]
360 ]
361 },
362 "display order":1,
363 "estimated parameters":52
364 },
365 "Nucleotide GTR":{
366 "AIC-c":2633.0046471406,
367 "Equilibrium frequencies": [
368 [0.3251262626262627],
369 [0.1799242424242424],
370 [0.2026515151515151],
371 [0.2922979797979798]
372 ],
373 "Log Likelihood":-1247.247280799152,
374 "Rate Distributions":{
375 "Substitution rate from nucleotide A to nucleotide C":0,
376 "Substitution rate from nucleotide A to nucleotide G":1,
377 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
378 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
379 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
380 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
381 },
382 "display order":0,
383 "estimated parameters":69
384 },
385 "RELAX alternative":{
386 "AIC-c":2539.023758734034,
387 "Log Likelihood":-1203.827668840701,
388 "Rate Distributions":{
389 "Reference":{
390 "0":{
391 "omega":0,
392 "proportion":0.3229316344832856
393 },
394 "1":{
395 "omega":0,
396 "proportion":0.6561871399951409
397 },
398 "2":{
399 "omega":2.618905128891877,
400 "proportion":0.02088122552157349
401 }
402 },
403 "Synonymous site-to-site rates":{
404 "0":{
405 "proportion":0,
406 "rate":0.8672539109745554
407 },
408 "1":{
409 "proportion":1,
410 "rate":1
411 },
412 "2":{
413 "proportion":0,
414 "rate":1.04385559910209
415 }
416 },
417 "Test":{
418 "0":{
419 "omega":0,
420 "proportion":0.3229316344832856
421 },
422 "1":{
423 "omega":0,
424 "proportion":0.6561871399951409
425 },
426 "2":{
427 "omega":887.8019782663979,
428 "proportion":0.02088122552157349
429 }
430 }
431 },
432 "display order":2,
433 "estimated parameters":65
434 },
435 "RELAX null":{
436 "AIC-c":2540.205243445127,
437 "Log Likelihood":-1205.43925064937,
438 "Rate Distributions":{
439 "Reference":{
440 "0":{
441 "omega":0.01761845549263694,
442 "proportion":0.1028887690453239
443 },
444 "1":{
445 "omega":0.1789488803563501,
446 "proportion":0.8141260406522884
447 },
448 "2":{
449 "omega":5.480099329809248,
450 "proportion":0.08298519030238755
451 }
452 },
453 "Synonymous site-to-site rates":{
454 "0":{
455 "proportion":0,
456 "rate":0.8690455710978635
457 },
458 "1":{
459 "proportion":1,
460 "rate":1
461 },
462 "2":{
463 "proportion":0,
464 "rate":1.043145103957073
465 }
466 },
467 "Test":{
468 "0":{
469 "omega":0.01761845549263694,
470 "proportion":0.1028887690453239
471 },
472 "1":{
473 "omega":0.1789488803563501,
474 "proportion":0.8141260406522884
475 },
476 "2":{
477 "omega":5.480099329809248,
478 "proportion":0.08298519030238755
479 }
480 }
481 },
482 "display order":3,
483 "estimated parameters":64
484 }
485 },
486 "input":{
487 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
488 "number of sequences":32,
489 "number of sites":198,
490 "partition count":1,
491 "trees":{
492 "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
493 }
494 },
495 "test results":{
496 "LRT":3.223163617336922,
497 "p-value":0.07260318641568564,
498 "relaxation or intensification parameter":7.051367447513434
499 },
500 "tested":{
501 "0":{
502 "Node20":"Test",
503 "Node38":"Reference",
504 "Node4":"Test",
505 "REFERENCE":"Unclassified",
506 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"Unclassified",
507 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"Unclassified",
508 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"Unclassified",
509 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"Unclassified",
510 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"Unclassified",
511 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"Unclassified",
512 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"Unclassified",
513 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"Unclassified",
514 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"Unclassified",
515 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"Unclassified",
516 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"Unclassified",
517 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"Unclassified",
518 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"Unclassified",
519 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"Unclassified",
520 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"Unclassified",
521 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"Unclassified",
522 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Unclassified",
523 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Unclassified",
524 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Unclassified",
525 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Unclassified",
526 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Unclassified",
527 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Unclassified",
528 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Unclassified",
529 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"Unclassified",
530 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"Unclassified",
531 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Unclassified",
532 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Unclassified",
533 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"Unclassified",
534 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"Unclassified",
535 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"Unclassified",
536 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Unclassified"
537 }
538 },
539 "timers":{
540 "Overall":{
541 "order":0,
542 "timer":67
543 },
544 "Preliminary model fitting":{
545 "order":1,
546 "timer":5
547 },
548 "RELAX alternative model fitting":{
549 "order":3,
550 "timer":50
551 },
552 "RELAX null model fitting":{
553 "order":4,
554 "timer":12
555 }
556 }
557 }