0000219: Failure in Reltime analysis error

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0000219

MEGA

Calculation Error

public

2016-07-17 16:38

2016-07-25 11:45

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

assigned

Resolution

open

Platform

Mac

OS X

Product Version

MEGA-CC 11 (command line version)

Target Version

Fixed in Version

Summary

0000219: Failure in Reltime analysis error

Description

I am attempting to construct a time tree based on RADseq data that has given us an alignment of 4.2 million nucleotides across 114 taxa with about 50% missing data. I have specified a maximum likelihood tree for the input. However I am getting an error "Error: Failure in Reltime analysis" when I attempt to use all sites.

Is there a limit to the size of the alignment for this type of analysis, and is that why I am getting this error? My alignment file is too large to upload to this form, 489 MB, but I can compress it to 125 MB and send it by another method if needed. When I attempted the analysis with complete deletion, there were no available sites. However, I was able to do the analysis with partial deletion, which resulted in 625 sites, but the tree was unresolved. Therefore, I would like to try it using all sites. Can you tell from the log below what this error means? Thanks.

Steps To Reproduce

megacc -a reltime_ml_VireyaRAD1to5.mao -d VireyaRAD1to5d6m4c90t58p5R1_only1bagjavs_ingroup_noRret1.fasta -t RAxML_bestTree.VireyaRAD1to5d6m4c90t58p5R1_only1bagjavs.fullmsa.rbsML.ingroup.noRret1.cnode.new -g groups.txt -c VireyaRAD1to5Calibration.txt -o VireyaRAD1to5.timeTree.test

MEGA-CC 7.0.18 Molecular Evolutionary Genetics Analysis
Build#: 7160617-x86_64
    0% Organizing sequence information a
    0% 17-7-16 16:00:12
Using the following analysis options:
  No. of Taxa 114
  No. of Groups 1
  Analysis Estimate Divergence Times (ML)
  Tree to Use Use tree from file
  Clock Type Local clocks
  Variance Estimation Method Analytical method
  No. of Bootstrap Replications Not Applicable
  Statistical Method Maximum Likelihood
  Substitutions Type Nucleotide
  Model/Method General Time Reversible model
  Rates among Sites Gamma Distributed (G)
  No of Discrete Gamma Categories 4
  Gaps/Missing Data Treatment Use all sites
  Site Coverage Cutoff (%) Not Applicable
  Branch Swap Filter None
  Number of Threads 1
  Has Time Limit False
  Maximum Execution Time -1
  datatype snNucleotide
  containsCodingNuc False
  MissingBaseSymbol ?
  IdenticalBaseSymbol .
  GapSymbol -
Start time: 17-7-16 16:00:12
Executing analysis:

    0% Setting model parameters MEGA-CC has logged the following error:
  When = 17-7-16 16:10:22
  Data file = VireyaRAD1to5d6m4c90t58p5R1_only1bagjavs_ingroup_noRret1.fasta
  AnalysisFile = ./reltime_ml_VireyaRAD1to5.mao
  Tree File = RAxML_bestTree.VireyaRAD1to5d6m4c90t58p5R1_only1bagjavs.fullmsa.rbsML.ingroup.noRret1.cnode.new
  Parameter = -t
  Parameter = RAxML_bestTree.VireyaRAD1to5d6m4c90t58p5R1_only1bagjavs.fullmsa.rbsML.ingroup.noRret1.cnode.new
  Parameter = -g
  Parameter = groups.txt
  Parameter = -c
  Parameter = VireyaRAD1to5Calibration.txt
  Parameter = -o
  Parameter = VireyaRAD1to5.timeTree.test
  Message = Failure in Reltime analysis

  Please see the summary file for warnings/messages
  Please validate all your inputs and try again. If you think this is a
  bug, please report it at http://www.megasoftware.net [^]

Additional Information

The various input files besides the alignment are shown below:

reltime_ml_VireyaRAD1to5.mao file:
; Please do not edit this file! If this file is modified, results are unpredictable.
; Instead of modifying this file, simply create a new MEGA Analysis Options file by using the MEGA Prototyper.
[ MEGAinfo ]
ver = 7160617-x86_64 Mac OS
[ DataSettings ]
datatype = snNucleotide
containsCodingNuc = False
MissingBaseSymbol = ?
IdenticalBaseSymbol = .
GapSymbol = -
[ ProcessTypes ]
ppRelTimeML = true
[ AnalysisSettings ]
Analysis = Estimate Divergence Times (ML)
Tree to Use = Use tree from file
Clock Settings = ====================
Clock Type = Local clocks
Variance Estimation Method = Analytical method
No. of Bootstrap Replications = Not Applicable
Statistical Method = Maximum Likelihood
Substitution Model = ====================
Substitutions Type = Nucleotide
Model/Method = General Time Reversible model
Rates and Patterns = ====================
Rates among Sites = Gamma Distributed (G)
No of Discrete Gamma Categories = 4
Data Subset to Use = ====================
Gaps/Missing Data Treatment = Use all sites
Site Coverage Cutoff (%) = Not Applicable
Branch Swap Filter = None
System Resource Usage = ====================
Number of Threads = 1
Has Time Limit = False
Maximum Execution Time = -1

RAxML_bestTree.VireyaRAD1to5d6m4c90t58p5R1_only1bagjavs.fullmsa.rbsML.ingroup.noRret1.cnode.new:
(((((((((((((((((((Rrho1combined:0.0010472915237878099,Rmai1combined:0.0017736383699860677):2.850973266885153E-4,Ralt1:0.0010039830053475115):1.520220441855767E-4,Rsol1combined:0.0015670415830772158):1.7296354962271284E-4,((Rbla2:7.548351223943598E-4,Rcul1combined:8.987085940989032E-4):3.2544066556271803E-4,Rfla1:0.0012841970679576516):1.648172167987546E-4):2.4713733899907656E-4,Rtub2combined:4.2517468458210634E-4):2.703719095856301E-4,(((Rpac1:5.488274917545687E-4,Rgar1:5.636313120496634E-4):5.205329084617727E-4,Rhel1:0.0011009447708972924):4.6417241955716153E-4,Rhya1:6.691545715146025E-4):1.5874401925806354E-4):8.137938015192161E-5,((((Rsea1combined:0.0022273552880784967,Rrap1:0.001150216776602365):4.4195295144916366E-4,(Raga3:0.0016873755883081315,Rher1:0.002341247894459472):3.050428818548188E-4):2.042052670038201E-4,((Rkonori79_036combined:0.0011008491786361706,Rsup3:9.119400683844077E-4):3.0197406543377634E-4,Rleu1:0.002230770561130692):4.7867611823196397E-4):1.1197686745114256E-4,(Rcar1combined:0.002019852675526222,Rgoo1:9.426011859818961E-4):3.9555268071130077E-4):1.3126235318316735E-4):9.989295941325452E-5,(Rlorl2:1.3094649076513342E-4,Rlur3:9.633596199602202E-4):0.0018795274920096272):1.1130880979937525E-4,((((((Rwen2:0.0026023630292778157,Rchr4:0.003473994906439371):3.095811975378531E-4,(Rzoe3combined:0.0011598672256221544,Rlae2combined:0.0020861997285405148):0.0011929998802519774):2.806552817693102E-4,(Rchr1combined:0.002935215202208182,Rsax1combined:0.0021245611851447247):2.0987292953048866E-4):1.6066005531516916E-4,Rmac1combined:0.002335159472174443):2.2057618791792904E-4,Rcom3:0.002276173294085785):2.1121701373059759E-4,(((Rinc1:0.0018153247718477256,Ryel1combined:0.0010646272740367057):0.0012144839007903869,Rwom1combined:4.812472639455456E-4):3.861677928233485E-4,Rloc3:0.001742543771996336):1.839659784963927E-4):1.5638846237608407E-4):2.960820720031416E-4,((((Rpha6:8.626219213493872E-4,Rlep1:8.926771535525824E-4):5.901545542281201E-4,Rbey2combined:0.0014355916864397006):3.173944559285991E-4,((Rrar9:0.0014370693612855829,Rcal1:0.0010495215685281379):5.646952228699997E-4,Rdied1:0.002439728570401776):2.2288272000815595E-4):1.85666296261117E-4,Rnsp2:0.0023600586004368894):1.6238499321025274E-4):3.821951945412552E-4,((((Rmus1:0.0019446844320598785,Rgra10:0.001592204872453006):2.8342719869467795E-4,Rana3:0.0024587083411112738):2.863333438275433E-4,(Rvit3:0.001965802004701245,Rrub3:0.0013935283701044926):1.6227743300458328E-4):3.5903689172501774E-4,Rwriw1:9.942645504034996E-4):3.757130493442696E-4):0.001889268317318003,Rlon3:0.0010623109216894731):0.0032735171733685327,((((((((Rrut2:0.0023703637968443747,Rrad2:0.0013633764527991254):0.0027463864324792004,(Rorb6:0.0017473463562009634,Rjasj2:0.0031490984459366734):7.19142578754893E-4):5.043078075871382E-4,(Rsua2:0.0018340797221713973,Redae2:0.0029722160259920507):0.001238645820559094):9.118830002150962E-4,Rpol1:0.00432569160855175):5.451034971507177E-4,Rsta1:0.0036995937633890535):5.927104339040984E-4,Rbur1:0.00450684956904491):4.574214729444317E-4,(((rugosum99_288combined:0.0011913243654534463,Rabi2combined:0.0014789097921968097):0.001035812206889665,Rpra1001:0.0023828090187740353):8.674072219521635E-4,Rbux1:0.003410716056724148):8.481726718164806E-4):5.23011386889252E-4,((Rtax1combined:0.0018616674806515698,Rvidv1combined:0.0027787747346098555):0.0018867003855572992,Rrou1:0.002577126388065908):0.0030755382289958345):0.0014221403348783448):7.214542793292997E-4,(((Rcit1combined:0.004087789639709654,Ralb5:0.0038046355549461635):3.1194041096066353E-4,Rban1:0.003417426348114278):6.092002386849851E-4,Rpau2:0.0025190454907518087):0.00448480198897287):7.007300987509964E-4,((((((((Rjavk3:0.0010777984108892376,Rjavb6:9.748884635954084E-4):3.295885743162375E-4,Rjavp5:0.0028648958770490763):2.588524104981461E-4,(Rjavc3:0.002203029926562736,Rjavs14:0.0038477070065553944):5.524848351054334E-4):6.249632579603792E-4,Rcra1:0.002335918123923633):4.929340433602105E-4,(Rlow3:0.002641621564735165,Rjavm5:0.0016243386116021868):0.0011227526992434633):4.3651576946384415E-4,((((((Rjavj1_3combined:0.0016650087158131593,Rmul5:0.0020167874811106764):4.160947994382293E-4,Rjavc4:0.0011832506530210438):3.770108690161394E-4,Rrob1001:0.0018592652592522494):3.05903080861873E-4,Rrar5:0.002009157968258074):8.661114584601349E-4,Rjavg9:0.0024554447632587793):0.001249609379856951,Racr8:0.004635630851748605):6.456084511475271E-4):4.6608158253124506E-4,((Rbag18:0.003908145831150283,Rstes4:0.0023742085775239124):0.0013770981024831025,Rlan1:0.0036173859110599275):5.544671063938869E-4):0.0013503015152956865,((((((Rrho3:0.002422649582846112,Rimp2:0.001329550925639406):2.6371396465810665E-4,(Rcel2combined:4.430349000007716E-4,Rlep3:5.103997500647779E-4):0.0015681618418676895):5.868101178283291E-4,Rkoc1:0.0030108184276435614):2.532438917861128E-4,(Rzol3:9.074764019153398E-4,Rlag2:9.352591628458341E-4):0.0021833448058678094):7.576856946655919E-4,Rbra1:0.003989811029377135):0.0016251457431395039,Rche1combined:0.004399706547204828):4.957409075625134E-4):0.0034647838237983884):0.0018238601009298808,(((Rlaml1:0.0030623716247473597,Rapo3:0.005465565861067488):6.29008080255327E-4,(Rvin1:0.00448420303403759,Rmal2:0.004445179115627764):6.739645568015843E-4):0.0011907049748353883,himantodes2007_020combined:0.006219335298458463):0.0025428586732708764):0.0041659346435420136,((((((Rpul1001:0.0030367791170667576,Rmel4:0.0051393752995865455):8.696306827975216E-4,Reri1001:0.002579993682841371):8.340672842715723E-4,Rquaq3:0.007824481514465536):8.789449834382646E-4,Rborv1combined:0.0044336313033335045):0.0029937046606229602,Rret1001:0.00859882167733246):0.0011896853314903467,(Rper3:0.0031485595691561614,Rsco5:0.0032988261870327633):0.0032672550912547747):0.001636020388338658):0.0015531558363821205,((rushforthii97_087combined:0.0015342120116956092,Rkaw4:0.0028437856553860403):0.002114496099313092,Rema1001:0.004037975005225216):0.005919711128308392):4.826319525627281E-4,(Rsan1:0.007750038472354483,Rvac2:0.006981259768514891):0.0029692236945800215)'VMRCA';

groups.txt:
Rvac2=outgroup

VireyaRAD1to5Calibration.txt:
!NodeName='VMRCA' minTime=14.5 maxTime=26.7;

Notes
(0003685) gstecher (administrator) 2016-07-25 11:45	Hi Valerie, I am writing in response to your question regarding the Reltime analysis in MEGA-CC. Yeah, it sounds like your data set may be too large for the analysis. You could try using the partial deletion option so that sites with reasonable coverage are included. -- Best regards, Glen Stecher

Issue History
Date Modified	Username	Field	Change
2016-07-17 16:38	guest	New Issue
2016-07-25 11:45	gstecher	Assigned To	=> gstecher
2016-07-25 11:45	gstecher	Status	new => assigned
2016-07-25 11:45	gstecher	Note Added: 0003685

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