Mercurial > repos > iuc > hyphy_sm19
diff test-data/summary/nsp8.RELAX.json @ 26:af92956bfe88 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 07:05:34 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.RELAX.json Wed Jun 09 07:05:34 2021 +0000 @@ -0,0 +1,557 @@ +{ + "Synonymous site-posteriors": [ +[1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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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, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197] + ], + "name":"relax.filter.default" + } + }, + "fits":{ + "MG94xREV with separate rates for branch sets":{ + "AIC-c":2512.992528250552, + "Equilibrium frequencies": [ +[0.03825952761243274], + [0.01370948533169502], + [0.0238326285579188], + [0.05169206288834598], + [0.02910782227384961], + [0.01043016700423795], + [0.01813184740308045], + [0.03932728586627101], + [0.01035067712195123], + [0.003708944282165923], + [0.006447644771501305], + [0.01398469573761802], + [0.0283653688047424], + [0.01016412464618009], + [0.01766935821790241], + [0.03832416445281453], + [0.01521889661505549], + [0.005453366858635389], + [0.009480156518454269], + [0.02056209812326697], + [0.01157852606970437], + [0.004148917752546374], + [0.007212496554133422], + [0.01564363009947405], + [0.00411729822204095], + [0.001475345962268018], + [0.002564747797779777], + [0.005562840210150803], + [0.01128319250724396], + [0.004043091272315801], + [0.007028527343480687], + [0.01524460789411934], + [0.03592403244011121], + [0.01287261047188149], + [0.02237780168434643], + [0.04853659885475865], + [0.02733097915424774], + [0.009793473186905268], + [0.01702501611901085], + [0.03692661100139533], + [0.009718835644621534], + [0.003482537371104292], + [0.0060540580187001], + [0.01313102107355921], + [0.02663384763763138], + [0.009543670983435077], + [0.01659075888876379], + [0.0359847236220365], + [0.00848480075962617], + [0.03199221880690793], + [0.01801483181642438], + [0.006455230577911434], + [0.01122180073845716], + [0.02433965804833868], + [0.002295465694104339], + [0.003990447484454917], + [0.008655128485630147], + [0.01755532734880559], + [0.00629057695692368], + [0.01093556617204019], + [0.02371882618448924] + ], + "Log Likelihood":-1204.057620165384, + "Rate Distributions":{ + "non-synonymous/synonymous rate ratio for *Reference*": [ +[0, 1] + ], + "non-synonymous/synonymous rate ratio for *Test*": [ +[21.18256670135096, 1] + ], + "non-synonymous/synonymous rate ratio for *Unclassified*": [ +[0.5156677179593993, 1] + ] + }, + "display order":1, + "estimated parameters":52 + }, + "Nucleotide GTR":{ + "AIC-c":2633.0046471406, + "Equilibrium frequencies": [ +[0.3251262626262627], + [0.1799242424242424], + [0.2026515151515151], + [0.2922979797979798] + ], + "Log Likelihood":-1247.247280799152, + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981, + "Substitution rate from nucleotide C to nucleotide G":1.129990583516242, + "Substitution rate from nucleotide C to nucleotide T":2.723444388603395, + "Substitution rate from nucleotide G to nucleotide T":1.720896006888861 + }, + "display order":0, + "estimated parameters":69 + }, + "RELAX alternative":{ + "AIC-c":2539.023758734034, + "Log Likelihood":-1203.827668840701, + "Rate Distributions":{ + "Reference":{ + "0":{ + "omega":0, + "proportion":0.3229316344832856 + }, + "1":{ + "omega":0, + "proportion":0.6561871399951409 + }, + "2":{ + "omega":2.618905128891877, + "proportion":0.02088122552157349 + } + }, + "Synonymous site-to-site rates":{ + "0":{ + "proportion":0, + "rate":0.8672539109745554 + }, + "1":{ + "proportion":1, + "rate":1 + }, + "2":{ + "proportion":0, + "rate":1.04385559910209 + } + }, + "Test":{ + "0":{ + "omega":0, + "proportion":0.3229316344832856 + }, + "1":{ + "omega":0, + "proportion":0.6561871399951409 + }, + "2":{ + "omega":887.8019782663979, + "proportion":0.02088122552157349 + } + } + }, + "display order":2, + "estimated parameters":65 + }, + "RELAX null":{ + "AIC-c":2540.205243445127, + "Log Likelihood":-1205.43925064937, + "Rate Distributions":{ + "Reference":{ + "0":{ + "omega":0.01761845549263694, + "proportion":0.1028887690453239 + }, + "1":{ + "omega":0.1789488803563501, + "proportion":0.8141260406522884 + }, + "2":{ + "omega":5.480099329809248, + "proportion":0.08298519030238755 + } + }, + "Synonymous site-to-site rates":{ + "0":{ + "proportion":0, + "rate":0.8690455710978635 + }, + "1":{ + "proportion":1, + "rate":1 + }, + "2":{ + "proportion":0, + "rate":1.043145103957073 + } + }, + "Test":{ + "0":{ + "omega":0.01761845549263694, + "proportion":0.1028887690453239 + }, + "1":{ + "omega":0.1789488803563501, + "proportion":0.8141260406522884 + }, + "2":{ + "omega":5.480099329809248, + "proportion":0.08298519030238755 + } + } + }, + "display order":3, + "estimated parameters":64 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas", + "number of sequences":32, + "number of sites":198, + "partition count":1, + "trees":{ + "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)" + } + }, + "test results":{ + "LRT":3.223163617336922, + "p-value":0.07260318641568564, + "relaxation or intensification parameter":7.051367447513434 + }, + "tested":{ + "0":{ + "Node20":"Test", + "Node38":"Reference", + "Node4":"Test", + "REFERENCE":"Unclassified", + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"Unclassified", + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"Unclassified", + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"Unclassified", + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"Unclassified", + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"Unclassified", + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"Unclassified", + "epi_isl_1543980_hCoV_19_Singapore_490_2021":"Unclassified", + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"Unclassified", + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"Unclassified", + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"Unclassified", + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"Unclassified", + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"Unclassified", + "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"Unclassified", + "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"Unclassified", + "epi_isl_1652105_hCoV_19_Singapore_561_2021":"Unclassified", + "epi_isl_1652118_hCoV_19_Singapore_575_2021":"Unclassified", + "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Unclassified", + "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Unclassified", + "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", + "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", + "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Unclassified", + "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", + "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", + "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", + "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", + "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", + "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", + "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", + "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", + "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", + "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" + } + }, + "timers":{ + "Overall":{ + "order":0, + "timer":67 + }, + "Preliminary model fitting":{ + "order":1, + "timer":5 + }, + "RELAX alternative model fitting":{ + "order":3, + "timer":50 + }, + "RELAX null model fitting":{ + "order":4, + "timer":12 + } + } +} \ No newline at end of file