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Description

Convert the log file generated by MCMC_SEQ to be readable by Tracer.

Usage

 

SummarizeMCMCResults -mode "Tracer" [-cl chainLength] [-bl burnInLength] [-sf sampleFrequency] [-outfile filename] [-truenet networkString]

Settings

-cl chainLength

The length of the MCMC chain. Set to the same value used in MCMC_SEQ.

required

-bl burnInLengthThe number of iterations in burn-in period. Set to the same value used in MCMC_SEQ.required

-sf sampleFrequency

The sample frequency. Set to the same value used in MCMC_SEQ.

required

-outfile filenameThe name of tracer log file you want to generate. Can contain path.required
-truenet networkString The network you want to summarize its parameters.required
 

 

Example

 

If we run MCMCseq_example1.nex , which is one of the example in the description of command MCMC_SEQ, we will get following output. Suppose it is printed into file example_mcmcseq_1.out.

Then the content of example_mcmcseq_1.out looks like:

 

 

MCMC_SEQ -cl 50000 -bl 10000 -sgt (gt0, gt1) -snet (net1) -sps 0.04 -pre 20
Output files under /Users/zhujiafan
SET _POP_SIZE_MEAN = 0.046099144360160785
SET _POP_SIZE_WINDOW_SIZE = 0.0023049572180080394
SET _TIME_WINDOW_SIZE = 0.0025150755969370955
----------------------- Logger: -----------------------
Iteration; Posterior; ESS; Likelihood; Prior; ESS; #Reticulation
1; -2370.95407; 0.00000; -2370.64467; -0.30939; 0.00000; 1;
[0.03712369495639094](((C:0.023825648320444256,B:0.023825648320444256)I2:0.050125924499740626)I3#H1:0.4705848357733278::0.4977571578778074,(A:0.09748469830982424,I3#H1:0.02353312548963936::0.5022428421221926)I1:0.44705171028368845)I0;
2; -2370.02122; 0.00000; -2365.48071; -4.54051; 0.00000; 1;
[0.08740412526529193](((A:0.0644782523371697)I3#H1:0.011085100576159218::0.7394821248524521,(B:0.012295023776453121,C:0.012295023776453121)I2:0.06326832913687579)I1:0.7099466953690496,I3#H1:0.7210317959452088::0.2605178751475479)I0;
3; -2372.45184; 1.00000; -2368.78300; -3.66884; 1.00000; 1;
[0.09033941530851464](((A:0.045146002769816694)I3#H1:0.007585944777036023::0.8848743613665822,(C:0.01813233140385818,B:0.01813233140385818)I2:0.03459961614299453)I1:3.898141499134046,I3#H1:3.905727443911082::0.11512563863341785)I0;
4; -2367.92188; 2.00000; -2365.28211; -2.63977; 2.00000; 1;
[0.07069491916656903](((B:0.00872426064648134,C:0.00872426064648134)I2:0.06083313993717342,(A:0.006588553878875061)I3#H1:0.06296884670477969::0.8996115971738128)I1:5.372106361639526,I3#H1:5.435075208344306::0.10038840282618722)I0;
5; -2370.70912; 3.00000; -2367.77665; -2.93247; 3.00000; 1;
[0.06524159621009873](((B:0.0020694551571076533,C:0.0020694551571076533)I2:0.05700062041463809,(A:0.05752026401374041)I3#H1:0.0015498115580053276::0.6506663662068655)I1:3.895283178099869,I3#H1:3.8968329896578746::0.34933363379313453)I0;
6; -2370.17278; 4.00000; -2367.72976; -2.44302; 4.00000; 1;
[0.08326098635086286](((B:0.01573581643597444,C:0.01573581643597444)I2:0.054166996949172486,(A:0.05445033542656785)I3#H1:0.01545247795857907::0.2708973259263968)I1:3.1609361182119855,I3#H1:3.1763885961705647::0.7291026740736032)I0;
7; -2375.23091; 5.00000; -2370.29901; -4.93190; 5.00000; 1;
[0.05379778176231088]((((C:0.00999397908818145,B:0.00999397908818145)I2:0.08374945041951844)I3#H1:0.006697029242945116::0.7206438532760768,A:0.100440458750645)I1:14.193400722603458,I3#H1:14.200097751846403::0.27935614672392317)I0;
8; -2367.29436; 6.00000; -2366.26747; -1.02688; 6.00000; 1;
[0.03543271735376193](((B:0.005849707761867801,C:0.005849707761867801)I2:0.07841641875267599,(A:0.01271426487814302)I3#H1:0.07155186163640077::0.8622136520013726)I1:4.6994134208375336,I3#H1:4.770965282473934::0.13778634799862743)I0;
9; -2373.22179; 7.00000; -2368.15899; -5.06280; 7.00000; 1;
[0.06618446114985434]((A:0.06301458366842101,((B:0.0020198944585432693,C:0.0020198944585432693)I2:0.00993963859785437)I3#H1:0.051055050612023374::0.8453466268608258)I1:5.141614377672805,I3#H1:5.1926694282848285::0.15465337313917416)I0;
10; -2378.18933; 8.00000; -2366.39462; -11.79471; 8.00000; 2;
[0.09440157575724482]((((((C:0.005310928295931936,B:0.005310928295931936)I2:0.05954064895844466,A:0.0648515772543766)I1:16.126610263480238)#H1:6.7365747769686415::0.20921855279391943)#H2:1.3049036309951738::0.8790975883804708,#H1:8.041478407963815::0.7907814472060806):0.9036343768434847,#H2:2.2085380078386585::0.1209024116195292)I0;
----------------------- Summarization: -----------------------
Burn-in = 10000, Chain length = 50000, Sample size = 8, Acceptance rate = 0.70918
--------------- Operations ---------------
Operation:NarrowNNI; Used:20970; Accepted:0 ACrate:0.0
Operation:Swap-Nodes; Used:2783; Accepted:611 ACrate:0.21954725116780452
Operation:SubtreeSlide; Used:20754; Accepted:6081 ACrate:0.29300375831165076
Operation:Scale-Time; Used:2201; Accepted:1484 ACrate:0.6742389822807815
Operation:Add-Reticulation; Used:258; Accepted:4 ACrate:0.015503875968992248
Operation:Slide-SubNet; Used:13653; Accepted:4412 ACrate:0.32315242071339634
Operation:TreeScaler; Used:5202; Accepted:2824 ACrate:0.5428681276432141
Operation:Flip-Reticulation; Used:804; Accepted:22 ACrate:0.02736318407960199
Operation:Change-PopSize-Prior-Param; Used:437; Accepted:220 ACrate:0.5034324942791762
Operation:Scale-Root-Time; Used:2722; Accepted:2350 ACrate:0.8633357825128581
Operation:Scale-PopSize-Prior-Param; Used:367; Accepted:327 ACrate:0.8910081743869209
Operation:Scale-All; Used:620; Accepted:72 ACrate:0.11612903225806452
Operation:Move-Head; Used:914; Accepted:163 ACrate:0.17833698030634573
Operation:TreeRootScaler; Used:5128; Accepted:1579 ACrate:0.3079173166926677
Operation:WildNNI; Used:5090; Accepted:0 ACrate:0.0
Operation:TNodeReheight; Used:41825; Accepted:6414 ACrate:0.15335325762104005
Operation:Change-Time; Used:15414; Accepted:7158 ACrate:0.464383028415726
Operation:Scale-PopSize; Used:549; Accepted:478 ACrate:0.8706739526411658
Operation:Change-Inheritance; Used:797; Accepted:443 ACrate:0.5558343789209536
Operation:Move-Tail; Used:2360; Accepted:26 ACrate:0.011016949152542373
Operation:Delete-Reticulation; Used:251; Accepted:3 ACrate:0.01195219123505976
Operation:WilsonBalding; Used:5250; Accepted:0 ACrate:0.0
Operation:Change-PopSize; Used:1651; Accepted:788 ACrate:0.47728649303452453

Overall MAP = -2367.294357178221
(((B:0.005849707761867801,C:0.005849707761867801)I2:0.07841641875267599,(A:0.01271426487814302)I3#H1:0.07155186163640077::0.8622136520013726)I1:4.6994134208375336,I3#H1:4.770965282473934::0.13778634799862743)I0;
-------------- 95% credible set of topologies --------------
Rank = 0; Size = 5; Percent = 62.50; MAP = -2367.294357178221:(((B:0.005849707761867801,C:0.005849707761867801)I2:0.07841641875267599,(A:0.01271426487814302)I3#H1:0.07155186163640077::0.8622136520013726)I1:4.6994134208375336,I3#H1:4.770965282473934::0.13778634799862743)I0; Ave=-2369.709994467344; ((A:0.03528388419342861)I3#H1:4.236997904111553::0.26626965889975657,((B:0.010102314281057883,C:0.010102314281057883)I2:0.057003358439330895,I3#H1:0.031821788526960174::0.7337303411002434)I1:4.205176115584593)I0;
Rank = 1; Size = 2; Percent = 25.00; MAP = -2373.221789051192:((A:0.06301458366842101,((B:0.0020198944585432693,C:0.0020198944585432693)I2:0.00993963859785437)I3#H1:0.051055050612023374::0.8453466268608258)I1:5.141614377672805,I3#H1:5.1926694282848285::0.15465337313917416)I0; Ave=-2374.2263488001636; (((B:0.0060069367733623594,C:0.0060069367733623594)I2:0.04684454450868641)I3#H1:9.696383590065615::0.13967807336196159,(A:0.081727521209533,I3#H1:0.028876039927484234::0.8603219266380384)I1:9.667507550138131)I0;
Rank = 2; Size = 1; Percent = 12.50; MAP = -2378.189329515679:((((((C:0.005310928295931936,B:0.005310928295931936)I2:0.05954064895844466,A:0.0648515772543766)I1:16.126610263480238)#H1:6.7365747769686415::0.20921855279391943)#H2:1.3049036309951738::0.8790975883804708,#H1:8.041478407963815::0.7907814472060806):0.9036343768434847,#H2:2.2085380078386585::0.1209024116195292)I0; Ave=-2378.189329515679; ((((A:0.0648515772543766,(B:0.005310928295931936,C:0.005310928295931936)I2:0.05954064895844466)I1:16.126610263480238)#H2:6.7365747769686415::0.20921855279391943)#H1:2.2085380078386585::0.1209024116195292,(#H2:8.041478407963815::0.7907814472060806,#H1:1.3049036309951738::0.8790975883804708):0.9036343768434847)I0;

Total elapsed time : 23.77700 s

 

Suppose we want to analyze the parameters of sampled top network, we can write such a NEXUS file. Note that the "truenet" string is copied from the "Rank = 0" network.

 

 

#NEXUS

BEGIN SETS;
/Users/zhujiafan/Documents/BioinfoData/Report/example_mcmcseq_1.out
END;

BEGIN PHYLONET;
SummarizeMCMCResults -cl 50000 -bl 10000 -sf 5000
-mode "Tracer"
-outfile "/Users/zhujiafan/Documents/BioinfoData/Report/report.txt"
-truenet "(((B:0.005849707761867801,C:0.005849707761867801)I2:0.07841641875267599,(A:0.01271426487814302)I3#H1:0.07155186163640077::0.8622136520013726)I1:4.6994134208375336,I3#H1:4.770965282473934::0.13778634799862743)I0; ";
END;

 

 Run this NEXUS file using PhyloNet. We will get file report.txt, which is readable by Tracer. 

 

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