Hi, I'm working on a MrBayes analysis which includes constraints. This is the MrBayes block:
begin mrbayes;
log start filename = Concatenado.txt;
set autoclose = yes;
charset 16s = 1-803;
charset 28s = 804-4084;
partition gene = 2:16s,28s;
set partition = gene;
constraint hiru -1 = Hiru1 Hiru2 Hiru3 Hiru4 Hiru5 Hiru6 Hiru7 Hiru8 Hiru9 Hiru10 Hiru11 Hiru12 Hiru13 Hiru14 Hiru15 Hiru16 Hiru17 Hiru18 Hiru19 Hiru20 Hiru21 Hiru22 Hiru23 Hiru24 Hiru25 Hiru26 Hiru27 Hiru28 Hiru29 Hiru30 Hiru31 Hiru32 Hiru33 Hiru34 Hiru35 Hiru36 Hiru37 Hiru38 Hiru39 Hiru40 Hiru41 Hiru42 Hiru43 Hiru44 Hiru45 Hiru46 Hiru47 Hiru48 Hiru49 Hiru50 Hiru51 Hiru52 Hiru53 Hiru54 Hiru55 Hiru56 Hiru57 Hiru58 Hiru59;
constraint hormo -1 = AILO1 ALE4 ALG1 ALIC1 BIO2 BNM1 BRU1 BSM1 COLBred CSEGpre CSEGred CTEMsam CTEOsam CTEUpre ECNG1 EMCNsam EMOL2 EPAR1 EPOL1 ESIG1 EVRN1 GHI2 GRA1 HEST1 HFLIX1 HMOI HRUD1 IGL1 IGROsam LAC2 LARR1 LOP1 MAJ2 MND2 MON2 NRIV4 ORD1 PIG1 QLL1 QUE1 RBAR1 ROUR1 SAN2 SGF1 SLINred TES1 TOR2 VIL2 VLNA1 VPJ1 XAN2;
constraint nohemi -1 = AILO1 ALE4 ALG1 ALIC1 BIO2 BNM1 BRU1 BSM1 COLBred CSEGpre CSEGred CTEMsam CTEOsam CTEUpre ECNG1 EMCNsam EMOL2 EPAR1 EPOL1 ESIG1 EVRN1 GHI2 GRA1 HEST1 HFLIX1 HMOI HRUD1 IGL1 IGROsam LARR1 LOP1 MAJ2 MON2 NRIV4 ORD1 PIG1 QLL1 QUE1 RBAR1 ROUR1 SAN2 SGF1 SLINred TES1 TOR2 VIL2 VLNA1 VPJ1 XAN2;
constraint noailo -1 = ALE4 ALG1 ALIC1 BIO2 BNM1 BRU1 BSM1 COLBred CSEGpre CSEGred CTEMsam CTEOsam CTEUpre ECNG1 EMCNsam EMOL2 EPAR1 EPOL1 ESIG1 EVRN1 GHI2 GRA1 HEST1 HFLIX1 HMOI HRUD1 IGL1 IGROsam LARR1 LOP1 MAJ2 MON2 NRIV4 ORD1 PIG1 QLL1 QUE1 RBAR1 ROUR1 SAN2 SGF1 SLINred TES1 TOR2 VIL2 VLNA1 VPJ1 XAN2;
constraint penin -1 = ALE4 ALIC1 BIO2 BRU1 BSM1 ECNG1 EMOL2 EPAR1 EPOL1 ESIG1 EVRN1 GRA1 HEST1 HFLIX1 HRUD1 LARR1 LOP1 MAJ2 MON2 NRIV4 PIG1 QLL1 QUE1 SAN2 TOR2 VLNA1;
constraint vygxanaislas -1 = ALG1 BNM1 COLBred CSEGpre CSEGred CTEMsam CTEOsam CTEUpre EMCNsam GHI2 HMOI IGL1 IGROsam ORD1 PIG1 RBAR1 ROUR1 SGF1 SLINred TES1 VIL2 VPJ1 XAN2;
constraint vygxana -1 = PIG1 SGF1 XAN2;
constraint islas -1 = ALG1 BNM1 COLBred CSEGpre CSEGred CTEMsam CTEOsam CTEUpre EMCNsam GHI2 HMOI IGL1 IGROsam ORD1 RBAR1 ROUR1 SLINred TES1 VIL2 VPJ1;
unlink statefreq = (all);
unlink revmat = (all);
unlink pinvar = (all);
unlink shape = (all);
lset applyto = (all) nst = 6 rates = invgamma;
prset topologypr = constraints (hiru,hormo,nohemi,noailo,penin,vygxanaislas,vygxana,islas);
mcmc ngen = 10000000 samplefreq = 4000 relburnin = no burnin = 2000;
sump relburnin = no burnin = 2000;
sumt relburnin = no burnin = 2000;
log stop;
END;
But I get the following error:
Error in command "Prset"
There was an error on at least one processor
The error occurred when reading char. 94 on line 16772
in the file 'infile.nex'
Error in command "Execute"
Do you know what's wrong with it? I have run previos analysis using the same function for constraints with no errors.
Thanks
Hi Daniel,
I don't have very big experience with MrBayes partitioning (your setting is impressive for me)..
but I have experience with this kind of error :) from my site it's look, that you are missing some character like ";" or "," etc.
check again your script, especially line 16772..and I am sure you will find mistake.
Good luck!
Tatiana
Along the lines of Christian's answer, should it be "topologypr" or "topology pr"?
It is "topologypr" indeed, acording to the Mrayes 3.2.5 command reference guide.
I already found the problem. A single species appeared in two mutualy exclusive constraints, making the function fail. Be careful with this in you own scripts.
Thanks a lot for your answers.
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