| Previous changeset 32:fc50c4bac0a3 (2021-11-27) Next changeset 34:b110a31a9c61 (2022-08-18) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a" |
|
modified:
hyphy_fel.xml macros.xml test-data/relax-out1.json test-data/relax-out2-1.json |
|
added:
test-data/absrel-out2.json |
|
removed:
test-data/relax-out2-2.json |
| b |
| diff -r fc50c4bac0a3 -r 8a6ef85b934d hyphy_fel.xml --- a/hyphy_fel.xml Sat Nov 27 11:31:22 2021 +0000 +++ b/hyphy_fel.xml Wed Mar 30 00:12:04 2022 +0000 |
| [ |
| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09"> <description>Fixed Effects Likelihood</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @SYMLINK_FILES@ @@ -15,6 +15,9 @@ @branch_options@ --srv '$include_srv' --pvalue '$p_value' + @resample@ + --precision $precision + $ci --output '$fel_output' @ERRORS@ ]]></command> @@ -27,6 +30,12 @@ <option value="Yes">Yes (recommended)</option> <option value="No">No</option> </param> + <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" /> + <expand macro="resample"/> + <param argument="--precision" type="select" label="Optimization precision for preliminary fits"> + <option value="standard">Standard</option> + <option value="reduced">Reduced for faster fitting</option> + </param> </inputs> <outputs> <data name="fel_output" format="hyphy_results.json" /> @@ -37,6 +46,13 @@ <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> <output name="fel_output" file="fel-out1.json" compare="sim_size"/> </test> + <test> + <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> + <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> + <param name="ci" value="true" /> + <param name="precision" value="reduced" /> + <output name="fel_output" file="fel-out1.json" compare="sim_size"/> + </test> </tests> <help><![CDATA[ FEL : Fixed effects likelihood |
| b |
| diff -r fc50c4bac0a3 -r 8a6ef85b934d macros.xml --- a/macros.xml Sat Nov 27 11:31:22 2021 +0000 +++ b/macros.xml Wed Mar 30 00:12:04 2022 +0000 |
| [ |
| @@ -1,5 +1,6 @@ <?xml version="1.0"?> <macros> + <token name="@TOOL_VERSION@">2.5.36</token> <xml name="inputs"> <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> @@ -144,7 +145,6 @@ <yield/> </citations> </xml> - <token name="@TOOL_VERSION@">2.5.31</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement> @@ -156,6 +156,16 @@ <filter>advanced['save_alternative_model']</filter> </data> </xml> + <xml name="resample"> + <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." /> + </xml> + <token name="@resample@"><![CDATA[ + #if $resample: + --resample $resample + #end if + ]]> + </token> + <token name="@INPUT_TREE@"><![CDATA[ #if $input_nhx: --tree input.nhx |
| b |
| diff -r fc50c4bac0a3 -r 8a6ef85b934d test-data/absrel-out2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-out2.json Wed Mar 30 00:12:04 2022 +0000 |
| [ |
| b'@@ -0,0 +1,535 @@\n+{\n+ "Synonymous site-posteriors": [\n+[0.2237313836650769, 0.07034985497742986, 0.07145045464678079, 0.162904629542773, 0.08696014489632299, 0.4973049561752621, 0.9385366945295869, 0.07695133428552869, 0.001997373788362212, 0.000990883865044414, 1.597366276160643e-05, 0.001639173387605954, 0.0006726936008082838, 0.0005936260958686961, 0.01218331055979857, 6.818341915747173e-05, 3.10538784980663e-05, 0.0003850280284965983, 1.706749658825067e-05, 1.954717668341298e-05, 5.757139486184149e-05, 5.547696233589325e-07, 0.1027014607202221, 0.0005061229953062066, 0.0002713590976491243, 0.01071054750911007, 0.01058998805403938, 0.001824707456373813, 0.1040310240977791, 0.007394679956619656, 0.01548570716335477, 0.0008559908124777675, 0.0001902341284497764, 0.04379131907975038, 0.0001602246750758031, 0.872186620749095, 0.007390732327759301, 0.06674897008912457, 0.06972624550033353, 0.09402374412106476, 0.1105108657459435, 0.01328650075574577, 0.0004656132149530012, 0.02510551997724948, 2.726156324850206e-05, 0.218781542689419, 0.006387422790697847, 0.007440221639665756, 0.05243297879242407, 0.1290026685674839, 0.6362466982390221, 0.8443663408237136, 0.0008463748207276134, 0.07321341035497612, 0.7855063534903601, 0.3150726276771443, 0.8508489144151971, 0.02756928287263707, 0.01299322935453241, 0.01615676639466097, 0.1381872019916541, 0.06580359020038734, 0.007948607169236543, 0.03623393203353259, 0.001127119071510586, 2.510588082439908e-07, 0.001198735279712407, 1.499028692444743e-05, 0.0007376828878749214, 0.0001439329508670455, 0.0003622577009774282, 0.02916632660997443, 0.09212248703639002, 7.45231360132705e-06, 0.2140082858090768, 0.009508570249567472, 0.5162459275326868, 0.001293919095115566, 0.8726414064830788, 0.0001302201041918639, 0.003094500709258363, 0.002116963683292442, 0.001652532423559578, 2.885330472177516e-05, 0.8679630109050446, 0.06064786452319544, 0.01926710656265205, 0.003438784053820811, 0.04592043108186669, 0.009356125116963642, 1.39030344053496e-06, 0.1492915058063837, 0.07707061704057379, 0.07475315743864808, 0.000302419021163877, 0.144336435993247, 0.003223470679335452, 0.03037745915910377, 0.0003011350589031628, 0.006808005110601785, 0.0008232735328502056, 0.03833979319278999, 9.698364220287434e-05, 0.004939487216502053, 6.693653877999158e-05, 0.02813691694081084, 9.485847293237623e-06, 9.213850857247055e-06, 0.0653963700817919, 3.36098340810195e-05, 0.3256932672291724, 4.035388925446032e-05, 0.04374256630355731, 0.0001602246750758031, 0.4014805201846622, 7.992404162601145e-05, 0.01019186788933821, 5.157202070064211e-05, 0.01632615592433439, 2.711206299164022e-05, 1.39112911627399e-05, 0.0001144909315662084, 0.0001470176943661007, 0.008065109594132992, 0.0001053551543690356, 0.09762185907634006, 0.2690693395574275, 2.306365194486018e-06, 0.001629982970373876, 0.0005166683932434172, 0.008811904607316576, 0.004707366984528872, 0.0005329112697905272, 0.004709232000043501, 5.309771784866412e-06, 0.02081799460860159, 0.01482206699240225, 0.02247987076174615, 0.03334725806979871, 0.5823700494422802, 0.6236724985801352, 0.0185646271114748, 0.1682321476102055, 0.5117950109841621, 0.02454309603098215, 0.01143016187387928, 0.03611174379314762, 0.001160042508580727, 0.008675955890656782, 0.0006207030249667641, 0.3189329652004703, 0.009022200481586255, 0.00453169826721376, 0.01175652549884987, 0.03798598471232684, 3.415462094795308e-05, 0.02071616557444895, 0.01314271860208286, 0.2919550074913849, 0.01463675769845591, 0.3808264251791824, 0.0005743039294857045, 0.0001968101730522108, 8.98952537201286e-05, 0.07242504371764499, 0.0003645543853153564, 0.3778182412645538, 6.623577458551056e-06, 0.423433584889663, 6.299717466720515e-06, 0.0002383566395190999, 0.05603244198717539, 0.001549983450584894, 0.002286903228642564, 0.05910553215170956, 0.1696354264894034, 0.008408717444453151, 0.1784153043909985, 0.005750339228228735, 0.1911339411346325, 2.211643409474936e-06, 0.0005399645955134869, 0.00037995024257006'..b'55364640413],\n+ [0.01055038238273567],\n+ [0.01311330258173711],\n+ [0.01100238215235291],\n+ [0.01931219560697892],\n+ [0.0157719705998612],\n+ [0.01960332955558842],\n+ [0.01644767379420349],\n+ [0.01965132601881859],\n+ [0.02049322866376102],\n+ [0.008933621043463411],\n+ [0.007295949736387736],\n+ [0.009068296583349953],\n+ [0.007608523013862737],\n+ [0.007628698224327205],\n+ [0.009481877006094248],\n+ [0.00795552712159237],\n+ [0.01396413011303752],\n+ [0.01140428846505027],\n+ [0.01417464125436193],\n+ [0.01189287130232129] \n+ ],\n+ "Log Likelihood":-3399.656647852504,\n+ "Rate Distributions":{\n+ "Per-branch delta":{\n+ "2.5%":0,\n+ "97.5%":10.66318587577853,\n+ "Mean":1.142287895998736,\n+ "Median":0.2080459069952131\n+ },\n+ "Per-branch omega":{\n+ "2.5%":0,\n+ "97.5%":2.028136557891868,\n+ "Mean":666666667.5178814,\n+ "Median":1\n+ },\n+ "Synonymous site-to-site rates":{\n+ "0":{\n+ "proportion":0.3499070593950995,\n+ "rate":0.3584907731592092\n+ },\n+ "1":{\n+ "proportion":0.5579704535685105,\n+ "rate":1.083607309819905\n+ },\n+ "2":{\n+ "proportion":0.09212248703639001,\n+ "rate":2.93023662601063\n+ }\n+ }\n+ },\n+ "display order":1,\n+ "estimated parameters":67\n+ },\n+ "Full adaptive model":{\n+ "AIC-c":6937.867430345418,\n+ "Log Likelihood":-3399.405413285916,\n+ "Rate Distributions":{\n+ },\n+ "display order":2,\n+ "estimated parameters":67\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.857288723968,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.321213744258,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,\n+ "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741\n+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "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)"\n+ }\n+ },\n+ "runtime":"2.5.36",\n+ "test results":{\n+ "P-value threshold":0.05,\n+ "positive test results":0,\n+ "tested":16\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node12":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node8":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Baseline model fitting":{\n+ "order":2,\n+ "timer":129\n+ },\n+ "Complexity analysis":{\n+ "order":3,\n+ "timer":406\n+ },\n+ "Full adaptive model fitting":{\n+ "order":4,\n+ "timer":46\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":1006\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":0\n+ },\n+ "Testing for selection":{\n+ "order":5,\n+ "timer":424\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r fc50c4bac0a3 -r 8a6ef85b934d test-data/relax-out1.json --- a/test-data/relax-out1.json Sat Nov 27 11:31:22 2021 +0000 +++ b/test-data/relax-out1.json Wed Mar 30 00:12:04 2022 +0000 |
| b |
| b'@@ -3,53 +3,53 @@\n "branch attributes":{\n "0":{\n "Baboon":{\n- "General descriptive":0.001858767762813579,\n- "MG94xREV with separate rates for branch sets":0.001769472024099301,\n- "Nucleotide GTR":0.001680040630127455,\n- "RELAX alternative":0.001872256662230973,\n- "RELAX null":0.001855569334462731,\n- "RELAX partitioned descriptive":0.001898170574782418,\n- "k (general descriptive)":0.09971581394819819,\n+ "General descriptive":0.001859058366368826,\n+ "MG94xREV with separate rates for branch sets":0.001769294089885709,\n+ "Nucleotide GTR":0.001685167654714891,\n+ "RELAX alternative":0.001873708670384941,\n+ "RELAX null":0.001859167714920677,\n+ "RELAX partitioned descriptive":0.001898817195216417,\n+ "k (general descriptive)":0.09969742933359635,\n "original name":"Baboon"\n },\n "Cat":{\n- "General descriptive":0.3644803308678196,\n- "MG94xREV with separate rates for branch sets":0.2796030091674721,\n- "Nucleotide GTR":0.2660909938917123,\n- "RELAX alternative":0.3689219388980864,\n- "RELAX null":0.3256077554105627,\n- "RELAX partitioned descriptive":0.3717219559832593,\n- "k (general descriptive)":2.314507643873676,\n+ "General descriptive":0.3650161006190072,\n+ "MG94xREV with separate rates for branch sets":0.2796018473093496,\n+ "Nucleotide GTR":0.2660536011315811,\n+ "RELAX alternative":0.3685874431614762,\n+ "RELAX null":0.3167334440346762,\n+ "RELAX partitioned descriptive":0.3719472357609613,\n+ "k (general descriptive)":2.319877215422834,\n "original name":"Cat"\n },\n "Chimp":{\n- "General descriptive":0.001848680051431209,\n- "MG94xREV with separate rates for branch sets":0.001825434296531533,\n- "Nucleotide GTR":0.001818373670119325,\n- "RELAX alternative":0.001831703934281931,\n- "RELAX null":0.00183525802483954,\n- "RELAX partitioned descriptive":0.001832717232153088,\n- "k (general descriptive)":5.261186652622472,\n+ "General descriptive":0.001895983937468787,\n+ "MG94xREV with separate rates for branch sets":0.001826027667597702,\n+ "Nucleotide GTR":0.001820258053351119,\n+ "RELAX alternative":0.001831530791728368,\n+ "RELAX null":0.001834052740714585,\n+ "RELAX partitioned descriptive":0.001832682515795942,\n+ "k (general descriptive)":5.158328270628251,\n "original name":"Chimp"\n },\n "Cow":{\n- "General descriptive":0.3733627618450006,\n- "MG94xREV with separate rates for branch sets":0.2520490246808783,\n- "Nucleotide GTR":0.2481025999892287,\n- "RELAX alternative":0.342739998512865,\n- "RELAX null":0.2948256709356563,\n- "RELAX partitioned descriptive":0.3466331923230422,\n- "k (general descriptive)":2.846155982935764,\n+ "General descriptive":0.3737128696500712,\n+ "MG94xREV with separate rates for branch sets":0.2521304147607955,\n+ "Nucleotide GTR":0.2480198736772598,\n+ "RELAX alternative":0.3426997068768813,\n+ "RELAX null":0.2931467439343907,\n+ "RELAX partitioned descriptive":0.3469082289876269,\n+ "k (general descriptive)":2.852150041266453,\n "original name":"Cow"\n },\n "Horse":{\n- "General descriptive":0.2802176313870697,\n- "MG94xREV with separate rates for branch sets":0.2158304510870495,\n- "Nucleotide GTR":0.2090310577070883,\n- "RELAX alternative":0.3058487498567987,\n- "RELAX null":0.2559911331878715,\n- "RELAX partitioned descriptive":0.3034694616209482,\n- "k (general descriptive)":1.926646959057857,\n+ "General descriptive":0.2804279827409984,\n+ "MG94xREV with separate rates for branch sets":0.2158535884657318,\n+ "Nucleotide GTR":0.2090998951755368,\n+ "RELAX alternative":0.3058441352816696,\n+ "RELAX null":0.2546949756245578,\n+ "RELAX partitioned descriptive":0.303551'..b'36478\n+ "omega":1.410337865928411e-20,\n+ "proportion":0.28512630848952\n },\n "2":{\n- "omega":3.69263720947284,\n- "proportion":0.3753613202723282\n+ "omega":3.213510017765925,\n+ "proportion":0.4496296443475419\n }\n },\n "Test":{\n "0":{\n- "omega":0.1150006822953211,\n- "proportion":0.542405144031307\n+ "omega":1.408928936991542e-20,\n+ "proportion":0.265244047162938\n },\n "1":{\n- "omega":0.2401508033814633,\n- "proportion":0.08223353569636478\n+ "omega":1.410337865928411e-20,\n+ "proportion":0.28512630848952\n },\n "2":{\n- "omega":3.69263720947284,\n- "proportion":0.3753613202723282\n+ "omega":3.213510017765925,\n+ "proportion":0.4496296443475419\n }\n }\n },\n@@ -393,35 +393,35 @@\n "estimated parameters":35\n },\n "RELAX partitioned descriptive":{\n- "AIC-c":6937.04707353565,\n- "Log Likelihood":-3427.626871923648,\n+ "AIC-c":6937.049237937651,\n+ "Log Likelihood":-3427.627954124649,\n "Rate Distributions":{\n "Reference":{\n "0":{\n- "omega":0.1943306885168281,\n- "proportion":0.3359458135547653\n+ "omega":0.1847557016619168,\n+ "proportion":0.4766160247339328\n },\n "1":{\n- "omega":0.2607558478587815,\n- "proportion":0.4332550437039296\n+ "omega":0.3367540359539261,\n+ "proportion":0.3005513276312735\n },\n "2":{\n- "omega":4.134271224300374,\n- "proportion":0.2307991427413052\n+ "omega":4.272816072857538,\n+ "proportion":0.2228326476347937\n }\n },\n "Test":{\n "0":{\n- "omega":0,\n- "proportion":0.4753488415962343\n+ "omega":1.127143149593234e-21,\n+ "proportion":0.2367540589657237\n },\n "1":{\n- "omega":0,\n- "proportion":0.03858318603767072\n+ "omega":1.128270292740756e-21,\n+ "proportion":0.2771164325302933\n },\n "2":{\n- "omega":6.017221959238516,\n- "proportion":0.486067972366095\n+ "omega":6.023626417874829,\n+ "proportion":0.4861295085039831\n }\n }\n },\n@@ -430,7 +430,7 @@\n }\n },\n "input":{\n- "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",\n+ "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",\n "number of sequences":10,\n "number of sites":187,\n "partition count":1,\n@@ -438,10 +438,11 @@\n "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)"\n }\n },\n+ "runtime":"2.5.32",\n "test results":{\n- "LRT":16.20300116404087,\n- "p-value":5.690389451429301e-05,\n- "relaxation or intensification parameter":2.344938789085876\n+ "LRT":16.80113246476958,\n+ "p-value":4.150852429507523e-05,\n+ "relaxation or intensification parameter":2.334214628944839\n },\n "tested":{\n "0":{\n@@ -466,11 +467,11 @@\n "timers":{\n "General descriptive model fitting":{\n "order":2,\n- "timer":132\n+ "timer":127\n },\n "Overall":{\n "order":0,\n- "timer":324\n+ "timer":396\n },\n "Preliminary model fitting":{\n "order":1,\n@@ -478,15 +479,15 @@\n },\n "RELAX alternative model fitting":{\n "order":3,\n- "timer":65\n+ "timer":103\n },\n "RELAX null model fitting":{\n "order":4,\n- "timer":66\n+ "timer":41\n },\n "RELAX partitioned descriptive":{\n "order":5,\n- "timer":53\n+ "timer":116\n }\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r fc50c4bac0a3 -r 8a6ef85b934d test-data/relax-out2-1.json --- a/test-data/relax-out2-1.json Sat Nov 27 11:31:22 2021 +0000 +++ b/test-data/relax-out2-1.json Wed Mar 30 00:12:04 2022 +0000 |
| [ |
| b'@@ -1,60 +1,60 @@\n {\n "Synonymous site-posteriors": [\n-[0.2717348381268465, 0.5635158143073038, 0.5580958985234344, 0.4419267392327456, 0.1775513314393873, 0.01303903284026798, 0.00125071980641974, 0.2376006215377312, 0.8837687913991302, 0.697488732253998, 0.76440666757549, 0.1859131352278527, 0.4676839084660329, 0.5320161033357819, 0.4513687349306337, 0.8514990846254493, 0.9101555767748879, 0.9112112654445478, 0.9624478616388369, 0.9472735837633918, 0.8715894173292342, 0.9248557783401865, 0.3852870058193366, 0.7504386709677574, 0.7275694213063354, 0.1979029930878776, 0.2585255313006612, 0.426812371619399, 0.03564414482172501, 0.3292941826787388, 0.1427864928730872, 0.8324822227281018, 0.9311167984186458, 0.1209539167468769, 0.8726642109588801, 1.798577785061191e-05, 0.584102863529593, 0.5747348035616634, 0.5814406651776627, 0.02251840852563282, 0.1607002230623373, 0.499402751628698, 0.9327364905381349, 0.1164578922551683, 0.7414294602970922, 0.04004321943657974, 0.1252919499200681, 0.7016909689123084, 0.3099147090319344, 0.1594271385761372, 0.001721088532959928, 0.0002106542138058178, 0.7670245595319366, 0.01765606757145387, 0.08528617939935416, 0.01185048796937841, 0.008218049898468071, 0.294285815926654, 0.4088819101657737, 0.1819814701794264, 0.06741006997792491, 0.1648869485561294, 0.6641637464726119, 0.1696421815033135, 0.5337345685031449, 0.9785329157950278, 0.6089117121305408, 0.9214198863478258, 0.7040511824729966, 0.8748810706893103, 0.7603207301908244, 0.1587648197710778, 0.28009015626025, 0.9473769917649164, 0.03667497185975328, 0.6646432746680839, 0.005707942217110617, 0.4172795698582943, 0.002426641321239203, 0.9036479890682162, 0.8165937919459629, 0.5380686752231248, 0.8348947378138256, 0.8825623566861087, 0.003194607014896987, 0.1034323185116836, 0.1251183560640448, 0.6731739154042389, 0.02049494631105097, 0.7272701824195644, 0.9376578101739967, 0.03161216349993828, 0.08060038603464466, 0.05713766811791781, 0.7236799166647727, 0.03049686563145122, 0.4831167820690108, 0.3259152163804719, 0.9355990871535625, 0.2598255955335131, 0.649043721535527, 0.1395744847880144, 0.8655465087299661, 0.5535165112383126, 0.8759601400318501, 0.1331847979385494, 0.9385179832315519, 0.9590294197009215, 0.1177725177949566, 0.5310119897564728, 0.04436932195281112, 0.877273324169318, 0.07309972300058731, 0.8726642109588801, 0.0823189228969842, 0.674523501474146, 0.4093792912564727, 0.8837869026711356, 0.1208432028324516, 0.7875716367935024, 0.9342090047974666, 0.7281976470761374, 0.6335560301454017, 0.2642816632435872, 0.7601746562441594, 0.3971532429331721, 0.07967254820654134, 0.9205611063156326, 0.4126590346311199, 0.4718488374006657, 0.2324587146851173, 0.2530879180545083, 0.6735650752750825, 0.6778765556227805, 0.9393601651000962, 0.1757530496502532, 0.3931715696771638, 0.7913247469383754, 0.05849180455884406, 0.007027787474985664, 0.002980098295172601, 0.188566078048928, 0.02837364230845984, 0.008078062694748547, 0.4539148488391334, 0.2698860362225194, 0.03514662617223248, 0.8484422182215356, 0.5225500090930265, 0.8755046006217432, 0.01843684138990366, 0.6656855504934923, 0.7055653078864003, 0.236066638653311, 0.1567944657161159, 0.8781825877891227, 0.4362059051173987, 0.163327088806649, 0.004489982631214889, 0.03278376720971195, 0.03145887036879619, 0.6158371404365816, 0.8645373560796752, 0.6351698115277034, 0.04852978149651612, 0.2563374460202912, 0.07868312568368593, 0.9507071563814276, 0.007940480658871889, 0.9455733391892027, 0.4761025393051341, 0.06329409664274364, 0.486108446887078, 0.6554607928409875, 0.3294403859657761, 0.02718898835050054, 0.2632599441236705, 0.09462189267290307, 0.2747185708643275, 0.01971954733787938, 0.9591589529807978, 0.445066915720239, 0.7380186230528726, 0.3686112558749921, 0.9765948224615983, 0.9830372572797934, 0.3428744949444181],\n- [0.6626894690463668, 0.4168101145890417, 0.4227716136375318, 0.5460469376257381, 0.7920802349484392, 0.9148946082433389, 0.6025519507878634, 0.757695330723024'..b'oportion":0.6330324513232739,\n- "rate":0.9729462345446451\n+ "proportion":0.633162055223991,\n+ "rate":0.9728788992663913\n },\n "2":{\n- "proportion":0.1028580221442092,\n- "rate":3.029415427453047\n+ "proportion":0.1025441367113787,\n+ "rate":3.038218152856258\n }\n },\n "Test":{\n "0":{\n "omega":0,\n- "proportion":0.04600287725570656\n+ "proportion":0.3885051761591228\n },\n "1":{\n- "omega":0,\n- "proportion":0.3432466763494891\n+ "omega":0.9958737025997172,\n+ "proportion":0\n },\n "2":{\n- "omega":1.896477292815783,\n- "proportion":0.6107504463948045\n+ "omega":1.887643080900262,\n+ "proportion":0.6114948238408772\n }\n }\n },\n "display order":3,\n- "estimated parameters":40\n+ "estimated parameters":44\n },\n "RELAX partitioned descriptive":{\n- "AIC-c":6909.42794543134,\n- "Log Likelihood":-3408.579104294618,\n+ "AIC-c":6917.810941882631,\n+ "Log Likelihood":-3408.559317095162,\n "Rate Distributions":{\n "Reference":{\n "0":{\n- "omega":0.05035684771569529,\n- "proportion":0.3805224005150026\n+ "omega":0.03550460650841439,\n+ "proportion":0.354985198548996\n },\n "1":{\n- "omega":0.07013486723985318,\n- "proportion":0.003462124163764896\n+ "omega":0.05439939847728128,\n+ "proportion":0.02231130867735708\n },\n "2":{\n- "omega":2.344944921144001,\n- "proportion":0.6160154753212325\n+ "omega":2.333762420535514,\n+ "proportion":0.6227034927736469\n }\n },\n "Test":{\n "0":{\n "omega":0,\n- "proportion":0.03160127773820932\n+ "proportion":0.3705590531463396\n },\n "1":{\n "omega":0,\n- "proportion":0.4079248249859382\n+ "proportion":0.06265340406614885\n },\n "2":{\n- "omega":1.11269394570475,\n- "proportion":0.5604738972758525\n+ "omega":1.08372848194659,\n+ "proportion":0.5667875427875115\n }\n }\n },\n "display order":5,\n- "estimated parameters":45\n+ "estimated parameters":49\n }\n },\n "input":{\n- "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/5/working/./input.nex",\n+ "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex",\n "number of sequences":10,\n "number of sites":187,\n "partition count":1,\n@@ -471,10 +471,11 @@\n "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)"\n }\n },\n+ "runtime":"2.5.32",\n "test results":{\n- "LRT":11.47546300090198,\n- "p-value":0.0007052107640865835,\n- "relaxation or intensification parameter":2.986519568748539e-05\n+ "LRT":11.58431319646934,\n+ "p-value":0.0006651049394417186,\n+ "relaxation or intensification parameter":3.335337302186161e-05\n },\n "tested":{\n "0":{\n@@ -499,11 +500,11 @@\n "timers":{\n "General descriptive model fitting":{\n "order":2,\n- "timer":127\n+ "timer":105\n },\n "Overall":{\n "order":0,\n- "timer":645\n+ "timer":3013\n },\n "Preliminary model fitting":{\n "order":1,\n@@ -511,15 +512,15 @@\n },\n "RELAX alternative model fitting":{\n "order":3,\n- "timer":178\n+ "timer":1229\n },\n "RELAX null model fitting":{\n "order":4,\n- "timer":115\n+ "timer":690\n },\n "RELAX partitioned descriptive":{\n "order":5,\n- "timer":216\n+ "timer":980\n }\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r fc50c4bac0a3 -r 8a6ef85b934d test-data/relax-out2-2.json --- a/test-data/relax-out2-2.json Sat Nov 27 11:31:22 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,3427 +0,0 @@\n-#NEXUS\n-\n-BEGIN TAXA;\n-\tDIMENSIONS NTAX = 10;\n-\tTAXLABELS\n-\t\t'HUMAN' 'CHIMP' 'BABOON' 'RHMONKEY' 'COW' 'PIG' 'HORSE' 'CAT' 'MOUSE' 'RAT' ;\n-END;\n-\n-BEGIN CHARACTERS;\n-\tDIMENSIONS NCHAR = 561;\n-\tFORMAT\n-\t\tDATATYPE = DNA\n-\t\tGAP=-\n-\t\tMISSING=?\n-\t;\n-\n-MATRIX\n-\t'HUMAN' AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n-\t'CHIMP' GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n-\t'BABOON' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n-\t'RHMONKEY' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n-\t'COW' ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT\n-\t'PIG' ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT\n-\t'HORSE' ------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATAT"..b'023*t*relax._shared_srv.rv_gdd*relax.test.theta_CT*relax.test.omega3;\n-relax.test_Q_component_3[60][56]:=0.1659124550130927*t*relax._shared_srv.rv_gdd*relax.test.theta_GT*relax.test.omega3;\n-relax.test_Q_component_3[60][57]:=0.2714859010999351*t*relax._shared_srv.rv_gdd*relax.test.theta_AT*relax.test.omega3;\n-relax.test_Q_component_3[60][58]:=0.2217183243979596*t*relax._shared_srv.rv_gdd*relax.test.theta_CT;\n-relax.test_Q_component_3[60][59]:=0.2755785876068215*t*relax._shared_srv.rv_gdd*relax.test.theta_GT*relax.test.omega3;\n-\n-\n-relax.test_pi={\n-{0.04876086397632926} \n-{0.03982224127745371} \n-{0.0494959405650269} \n-{0.04152830682371345} \n-{0.01810345074594235} \n-{0.01478480742075003} \n-{0.01837636270304883} \n-{0.01541821854326533} \n-{0.01892910005547028} \n-{0.01545910240515689} \n-{0.01921445878706794} \n-{0.01612140169177368} \n-{0.02829747763884322} \n-{0.02311011106415996} \n-{0.02872406592369408} \n-{0.02410019507229243} \n-{0.01663805943190806} \n-{0.01358804506433061} \n-{0.01688888041768248} \n-{0.01417018446135155} \n-{0.006177213955434187} \n-{0.005044834822351987} \n-{0.006270336287397383} \n-{0.00526096577332031} \n-{0.006458939937330408} \n-{0.005274916061901906} \n-{0.006556309326397028} \n-{0.005500904159606446} \n-{0.009655594186286731} \n-{0.007885574003572761} \n-{0.009801153568494354} \n-{0.008223407979974132} \n-{0.03327785448210915} \n-{0.02717750758119989} \n-{0.03377952261833742} \n-{0.02834184710178207} \n-{0.01235507229404208} \n-{0.01009019590244688} \n-{0.01254132667213156} \n-{0.01052248035033209} \n-{0.01291855364640413} \n-{0.01055038238273567} \n-{0.01311330258173711} \n-{0.01100238215235291} \n-{0.01931219560697892} \n-{0.0157719705998612} \n-{0.01960332955558842} \n-{0.01644767379420349} \n-{0.01965132601881859} \n-{0.02049322866376102} \n-{0.008933621043463411} \n-{0.007295949736387736} \n-{0.009068296583349953} \n-{0.007608523013862737} \n-{0.007628698224327205} \n-{0.009481877006094248} \n-{0.00795552712159237} \n-{0.01396413011303752} \n-{0.01140428846505027} \n-{0.01417464125436193} \n-{0.01189287130232129} \n-};\n-Model relax.test=(\'Exp(relax.test_Q_component_1)*1*relax.test.bsrel_mixture_aux_0+Exp(relax.test_Q_component_2)*1*(1-relax.test.bsrel_mixture_aux_0)*relax.test.bsrel_mixture_aux_1+Exp(relax.test_Q_component_3)*1*(1-relax.test.bsrel_mixture_aux_0)*(1-relax.test.bsrel_mixture_aux_1)\',relax.test_pi,EXPLICIT_FORM_MATRIX_EXPONENTIAL);\n-TRY_NUMERIC_SEQUENCE_MATCH=0;\n-ACCEPT_ROOTED_TREES=0;\n-Tree O_SJmzEX.tree_id_0=((((PIG{relax.reference},COW{relax.reference})Node3{relax.reference},HORSE{relax.reference},CAT{relax.reference})Node2{relax.reference},((RHMONKEY{relax.test},BABOON{relax.test})Node9{relax.test},(HUMAN{relax.test},CHIMP{relax.test})Node12{relax.test})Node8{relax.test})Node1{relax.test},RAT{relax.reference},MOUSE{relax.reference});\n-\n-O_SJmzEX.tree_id_0.PIG.t=0.4536172365685577;\n-O_SJmzEX.tree_id_0.COW.t=0.6103212983838633;\n-O_SJmzEX.tree_id_0.Node3.t=0.2484758643179366;\n-O_SJmzEX.tree_id_0.HORSE.t=0.4753747079725157;\n-O_SJmzEX.tree_id_0.CAT.t=0.6775352409130856;\n-O_SJmzEX.tree_id_0.Node2.t=0.1183276378467358;\n-O_SJmzEX.tree_id_0.RHMONKEY.t=0.01420592464486799;\n-O_SJmzEX.tree_id_0.BABOON.t=0.00485857082125907;\n-O_SJmzEX.tree_id_0.Node9.t=0.1015257435189256;\n-O_SJmzEX.tree_id_0.HUMAN.t=0;\n-O_SJmzEX.tree_id_0.CHIMP.t=0.006303088015069631;\n-O_SJmzEX.tree_id_0.Node12.t=0.05697754732758539;\n-O_SJmzEX.tree_id_0.Node8.t=0.4948729770972781;\n-O_SJmzEX.tree_id_0.Node1.t=1.445991686991002;\n-O_SJmzEX.tree_id_0.RAT.t=0.1315597576696033;\n-O_SJmzEX.tree_id_0.MOUSE.t=0.2736332745970835;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n-SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);\n-\n-DataSet relax.codon_data = ReadDataFile(USE_NEXUS_FILE_DATA);\n-DataSetFilter relax.filter.default = CreateFilter(relax.codon_data,3,"0-560","5,4,6,7,3,2,0,1,9,8","TAA,TAG,TGA");\n-ASSUME_REVERSIBLE_MODELS=1;\n-USE_LAST_RESULTS=0;\n-LikelihoodFunction O_SJmzEX.likelihoodFunction = (relax.filter.default,O_SJmzEX.tree_id_0);\n-\n-END;\n\\ No newline at end of file\n' |