"Could not find a proper state to initialise" error

[Norm]

Hi, 

I've been having a hard time tracking down the errors when trying to run *BEAST.

The first mistake I had was that not every species was represented in every alignment. I rectified that in a quick and dirty way, by adding a single dummy sequence assigned to each species. Everything else is set according to the *BEAST tutorial. There is a fair amount of missing data in these alignments, since it was from a sequence-capture experiment. I'm just hoping that it's an error in the settings, and not a problem with trying to analyze this particular dataset. 

I will attach the xml. 

Thanks for any advice!

======================================================

Start likelihood: -Infinity after 11 initialisation attempts

P(posterior) = -Infinity (was NaN)

P(speciescoalescent) = -3.3262019264778784E11 (was NaN)

P(SpeciesTreePopSize.Species) = 690.8014759618696 (was NaN)

P(treePrior.t:AT1G01290dum_aln) = -9.642816448055316E10 (was NaN)

P(treePrior.t:AT1G12800dum_aln) = -1.2771911205960396E11 (was NaN)

P(treePrior.t:AT1G18190dum_aln) = -1.0847291679843216E11 (was NaN)

P(prior) = -Infinity (was NaN)

P(YuleModel.t:Species) = 211.30666951105965 (was NaN)

P(YuleBirthRatePrior.t:Species) = -5.362240542149371 (was NaN)

P(ClockPrior.c:AT1G01290dum_aln) = 0.0 (was NaN)

P(ClockPrior.c:AT1G18190dum_aln) = 0.0 (was NaN)

P(KappaPrior.s:AT1G01290dum_aln) = -1.8653600339742873 (was NaN)

P(KappaPrior.s:AT1G12800dum_aln) = -1.8653600339742873 (was NaN)

P(KappaPrior.s:AT1G18190dum_aln) = -1.8653600339742873 (was NaN)

P(popMean.prior) = 0.0 (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.AT1G12800dum_aln) = NaN (was NaN)

P(treeLikelihood.AT1G18190dum_aln) = NaN (was NaN)

P(treeLikelihood.AT1G01290dum_aln) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

[Remco Bouckaert]

Hi Norm,

The problem is that the birth-rate is initialised automatically, and gets assigned a value outside the range 0 to 10000 specified in the XML. If you set the upper bound on the birth-rate to 1E10 (you can edit the XML so it reads)

        <parameter id="birthRate.t:Species" lower="0.0" name="stateNode" upper="1e10">213.2021</parameter>

it should start. This issue is fixed for the next release.

Cheers,

Remco

[Norm]

Hmm. I made that edit and got the same error. Do you see another possibility?

[Remco Bouckaert]

That is strange -- I have no problem starting the chain, and tried a variety of seeds.

Perhaps try increasing the upper bound more, or remove the upper bound altogether.

Remco

[Norm]

OK, running now. I guess I changed a bad copy. Thank you!

[Mark]

Hi Remco,

I have a similar problem for which this patch was not a solution.  The "start likelihood" reported NaN.  Here is the relevant part of the log and I've attached my xml file.

many thanks!

Mark

Start likelihood: NaN 

P(posterior) = NaN (was NaN)

P(speciescoalescent) = NaN (was NaN)

P(SpeciesTreePopSize.Species) = NaN (was NaN)

P(treePrior.t:07cpmatch) = NaN (was NaN)

P(treePrior.t:08cpmatch) = NaN (was NaN)

P(treePrior.t:11cpmatch) = NaN (was NaN)

P(treePrior.t:SDC_cp nosXa) = NaN (was NaN)

P(prior) = NaN (was NaN)

P(YuleModel.t:Species) = NaN (was NaN)

P(YuleBirthRatePrior.t:Species) = -5.362240542149371 (was NaN)

P(ClockPrior.c:08cpmatch) = 0.0 (was NaN)

P(ClockPrior.c:11cpmatch) = 0.0 (was NaN)

P(ClockPrior.c:SDC_cp nosXa) = 0.0 (was NaN)

P(GammaShapePrior.s:07cpmatch) = -1.0 (was NaN)

P(GammaShapePrior.s:08cpmatch) = -1.0 (was NaN)

P(GammaShapePrior.s:11cpmatch) = -1.0 (was NaN)

P(GammaShapePrior.s:SDC_cp nosXa) = -1.0 (was NaN)

P(KappaPrior.s:07cpmatch) = -1.8653600339742873 (was NaN)

P(MutationRatePrior.s:07cpmatch) = 0.0 (was NaN)

P(MutationRatePrior.s:08cpmatch) = 0.0 (was NaN)

P(MutationRatePrior.s:11cpmatch) = 0.0 (was NaN)

P(MutationRatePrior.s:SDC_cp nosXa) = 0.0 (was NaN)

P(popMean.prior) = 0.0 (was NaN)

P(RateACPrior.s:08cpmatch) = -3.184008455701433 (was NaN)

P(RateACPrior.s:11cpmatch) = -3.184008455701433 (was NaN)

P(RateACPrior.s:SDC_cp nosXa) = -3.184008455701433 (was NaN)

P(RateAGPrior.s:08cpmatch) = -3.1686658147294304 (was NaN)

P(RateAGPrior.s:11cpmatch) = -3.1686658147294304 (was NaN)

P(RateAGPrior.s:SDC_cp nosXa) = -3.1686658147294304 (was NaN)

P(RateATPrior.s:08cpmatch) = -3.184008455701433 (was NaN)

P(RateATPrior.s:11cpmatch) = -3.184008455701433 (was NaN)

P(RateATPrior.s:SDC_cp nosXa) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:08cpmatch) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:11cpmatch) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:SDC_cp nosXa) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:08cpmatch) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:11cpmatch) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:SDC_cp nosXa) = -3.184008455701433 (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.07cpmatch) = NaN (was NaN)

P(treeLikelihood.08cpmatch) = NaN (was NaN)

P(treeLikelihood.11cpmatch) = NaN (was NaN)

P(treeLikelihood.SDC_cp nosXa) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at apple.launcher.LaunchRunner.run(LaunchRunner.java:116)

at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:51)

at apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)

[Remco Bouckaert]

Hi Mark,

The issue is that there are taxa in the species tree that are not represented by all gene tree. For example, alignment "SDC_cp nosXa" has no sequences for species "y". It does contain "syr4885_cp" that is currently part of species "s", so perhaps that was not what was intended?

Cheers,

Remco

[Mark]

Thanks Remco!  I should have caught that--it was staring right at me.  You are exactly right.  I am running.

cheers,

Mark

[石勇]

Hi, Remco

      Did you mean that all the sequences number should be the same  for  the same species?

在 2014年7月16日星期三UTC+8上午4时17分41秒，Remco Bouckaert写道：

[Susana Magallon]

[Maca]

Hello everyone,

I am having a similar problem. I have tried all the possible fixes suggested on this (and other) posts but can't find the problem!

Could someone please help me?

Here is the error I am getting (xml attached)

Start likelihood: NaN 

P(posterior) = NaN (was NaN)

P(speciescoalescent) = NaN (was NaN)

P(SpeciesTreePopSize.Species) = NaN (was NaN)

P(treePrior.t:141121_Oreobolus_ITS) = NaN (was NaN)

P(treePrior.t:141121_Oreobolus_rpl32trnL) = NaN (was NaN)

P(treePrior.t:141121_Oreobolus_trnHpsbA) = NaN (was NaN)

P(treePrior.t:141121_Oreobolus_trnLF) = NaN (was NaN)

P(prior) = NaN (was NaN)

P(BirthDeath.t:Species) = NaN (was NaN)

P(BirthRatePrior.t:Species) = -23.025850929940457 (was NaN)

P(popMean.prior) = 0.0 (was NaN)

P(DeathRatePrior.t:Species) = 0.0 (was NaN)

P(MeanRatePrior.c:141121_Oreobolus_ITS) = 0.0 (was NaN)

P(MeanRatePrior.c:141121_Oreobolus_rpl32trnL) = 0.0 (was NaN)

P(MeanRatePrior.c:141121_Oreobolus_trnHpsbA) = 0.0 (was NaN)

P(MeanRatePrior.c:141121_Oreobolus_trnLF) = 0.0 (was NaN)

P(ucldStdevPrior.c:141121_Oreobolus_ITS) = -0.40143772133305716 (was NaN)

P(ucldStdevPrior.c:141121_Oreobolus_rpl32trnL) = -0.40143772133305716 (was NaN)

P(ucldStdevPrior.c:141121_Oreobolus_trnHpsbA) = -0.40143772133305716 (was NaN)

P(ucldStdevPrior.c:141121_Oreobolus_trnLF) = -0.40143772133305716 (was NaN)

P(rootAge.prior) = NaN (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.141121_Oreobolus_ITS) = NaN (was NaN)

P(treeLikelihood.141121_Oreobolus_rpl32trnL) = NaN (was NaN)

P(treeLikelihood.141121_Oreobolus_trnHpsbA) = NaN (was NaN)

P(treeLikelihood.141121_Oreobolus_trnLF) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

Many thanks for your help,

Maca

[Remco Bouckaert]

Hi Maca,

It looks like the problem with the test file you posted is that gene tree Tree.t:141121_Oreobolus_trnHpsbA has no lineages for species taxon Oreobolussp and a *BEAST analysis requires all taxa in the species tree to be represented in each gene tree by at least one sequence. If you add a sequence to the 141121_Oreobolus_trnHpsbA alignment for Oreobolussp (or just add a sequence with all question marks) as well as to the other alignment that currently have no sequence for Oreobolussp it runs.

Cheers,

Remco

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<test1.xml>

[Maca]

Hi Remco,

As someone said earlier on this post, it was staring at my face!

Many thanks for your help, running now.

Cheers,

Maca

[Michael Forthman]

Hello Remco,

Your help with fixing my starting tree topology was very helpful. Now, I have a different problem that is related to this thread. Below is the relevant information. I tried looking at my xml file while looking at previous posts, but they didn't seem to help in my situation.

Cheers, Michael

Start likelihood: -Infinity after 11 initialisation attempts

P(posterior) = -Infinity (was NaN)

P(prior) = -Infinity (was NaN)

P(YuleModel.t:18S_G_INS_i_aligned) = -59.36778300682473 (was NaN)

P(YuleBirthRatePrior.t:18S_G_INS_i_aligned) = 0.0 (was NaN)

P(GammaShapePrior.s:18S_G_INS_i_aligned) = -1.0 (was NaN)

P(MutationRatePrior.s:18S_G_INS_i_aligned) = 0.0 (was NaN)

P(RateACPrior.s:18S_G_INS_i_aligned) = -3.184008455701433 (was NaN)

P(RateAGPrior.s:18S_G_INS_i_aligned) = -3.1686658147294304 (was NaN)

P(RateATPrior.s:18S_G_INS_i_aligned) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:18S_G_INS_i_aligned) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:18S_G_INS_i_aligned) = -3.184008455701433 (was NaN)

P(MeanRatePrior.c:18S_G_INS_i_aligned) = 0.0 (was NaN)

P(MeanRatePrior.c:28S_D2_G_INS_i_aligned) = 0.0 (was NaN)

P(MeanRatePrior.c:28S_D3_5_G_INS_i_aligned) = 0.0 (was NaN)

P(MeanRatePrior.c:COI_G_INS_i_aligned) = 0.0 (was NaN)

P(ucldStdevPrior.c:18S_G_INS_i_aligned) = -0.40143772133305716 (was NaN)

P(ucldStdevPrior.c:28S_D2_G_INS_i_aligned) = -0.40143772133305716 (was NaN)

P(ucldStdevPrior.c:28S_D3_5_G_INS_i_aligned) = -0.40143772133305716 (was NaN)

P(ucldStdevPrior.c:COI_G_INS_i_aligned) = -0.40143772133305716 (was NaN)

P(Apicrenus.prior) = -Infinity (was NaN)

P(EctTrib.prior) = NaN (was NaN)

P(Outgroupsetting.prior) = NaN (was NaN)

P(Triatoma.prior) = NaN (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.18S_G_INS_i_aligned) = NaN (was NaN)

P(treeLikelihood.28S_D2_G_INS_i_aligned) = NaN (was NaN)

P(treeLikelihood.28S_D3_5_G_INS_i_aligned) = NaN (was NaN)

P(treeLikelihood.COI_G_INS_i_aligned) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

[Remco Bouckaert]

Hi Michael,

This line

P(Apicrenus.prior) = -Infinity (was NaN)

suggests that the starting tree somehow violates the Apicrenus prior. Most commonly, this is because the clade is not monophyletic in the starting tree (if the prior specifies monophyly), or because the prior is a calibration and the height of the clade is outside the range specified by the distribution for the calibration.

Hope this helps,

Remco

[Michael Forthman]

Thank Remco for the information. The starting tree has the clade, and I double checked the taxa included for the prior and that seems good. So it must be the calibration distribution vs. clade height. What is the most common practice to correct for this, if one exists?

Cheers, Michael

[Michael Forthman]

I can also attach my .xml file (privately) if it would assist.

Cheers, Michael

[Samuel Brown]

Hello all

It's a brand new year, and I've been unfortunate enough to run into BEAST problems already.

I'm attempting to run a STARBEAST analysis with 108 taxa and 4 genes. I've checked and rechecked that all taxa have all genes, so I'll be mighty embarrassed if that turns out to be the problem. I've constrained the ingroup to be monophyletic, and have specified an appropriate starting topology (a random tree with branch lengths modified to suit the dating constraint). My interpretation of the output (below) suggests that the starting tree is working OK (though I'll be happy to be corrected!).

However, it is still not finding a proper state to initialise. Any further ideas would be most welcome.

Thanks a lot!

Sam


======================================================

Start likelihood: NaN
P(posterior) = NaN (was NaN)

    P(speciescoalescent) = -2.0194161367026478E7 (was NaN)
        P(SpeciesTreePopSize.Species) = -215.0 (was NaN)
        P(treePrior.t:28S) = -3425861.898696659 (was NaN)
        P(treePrior.t:argk) = -2694722.28673329 (was NaN)
        P(treePrior.t:cad) = -2274691.2763185273 (was NaN)
        P(treePrior.t:coi3p) = -1.1798670905278001E7 (was NaN)
    P(prior) = -615.5401588595314 (was NaN)
        P(BirthDeath.t:Species) = -568.4144685480878 (was NaN)
        P(BirthRatePrior.t:Species) = -6.907755278982137 (was NaN)

        P(popMean.prior) = 0.0 (was NaN)

        P(DeathRatePrior.t:Species) = 0.0 (was NaN)
        P(MeanRatePrior.c:argk) = 0.0 (was NaN)
        P(MeanRatePrior.c:cad) = 0.0 (was NaN)
        P(MeanRatePrior.c:coi3p) = 0.0 (was NaN)
        P(entiminae.prior) = -4.6778156894421485 (was NaN)
        P(KappaPrior.s:28S) = -1.8653600339742873 (was NaN)
        P(RateACPrior.s:argk) = -3.184008455701433 (was NaN)
        P(RateAGPrior.s:argk) = -3.1686658147294304 (was NaN)
        P(RateATPrior.s:argk) = -3.184008455701433 (was NaN)
        P(RateCGPrior.s:argk) = -3.184008455701433 (was NaN)
        P(RateGTPrior.s:argk) = -3.184008455701433 (was NaN)
        P(RateACPrior.s:coi3p) = -3.184008455701433 (was NaN)
        P(RateAGPrior.s:coi3p) = -3.1686658147294304 (was NaN)
        P(RateATPrior.s:coi3p) = -3.184008455701433 (was NaN)
        P(RateCGPrior.s:coi3p) = -3.184008455701433 (was NaN)
        P(RateGTPrior.s:coi3p) = -3.184008455701433 (was NaN)
        P(KappaPrior.s:cad) = -1.8653600339742873 (was NaN)
        P(MeanRatePrior.c:28S) = 0.0 (was NaN)

    P(likelihood) = NaN (was NaN)

        P(treeLikelihood.28S) = NaN (was NaN)
        P(treeLikelihood.argk) = NaN (was NaN)
        P(treeLikelihood.cad) = NaN (was NaN)
        P(treeLikelihood.coi3p) = NaN (was NaN)

[Remco Bouckaert]

Hi Sam,

The problem with the XML is that the clock models use normal distributions — I don’t know how to do this in BEAUti so perhaps you edited the XML by hand? Since normal distributions have a range that include negative numbers, the rate can become negative. The branch rate is multiplied by the branch length to get al time of evolution over the branch, which can now become negative, leading to NaN’s in the tree likelihoods.

Perhaps you meant to use a log-normal distribution instead of a normal one in the relaxed clocks?

Cheers,

Remco

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<FailingToInitialise.xml>

[Samuel Brown]

Hi Remco

Thank you so much---changing the clock models from normal distributions to log-normal worked a treat.

In BEAUti it is possible to change the distribution of the clock model in the appropriate tab. I must've played with that a bit, and forgot what the default was (I guess a big hint was in the name---what's the logical choice for a "Log normal" relaxed clock?). Your explanation for the reason behind a normal distribution not working (especially that distribution I had given it) is very useful.

Thank you very much once again. It's saved me a lot of time and frustration.

Sam

[Catherine C]

Hi there,

I've been coming across the same error message - I've worked through the tutorial, and am now using my own dataset. I've gone back to trying the same priors and settings as in the tutorial on my own dataset as I was getting the error when I tried the priors and models that I wanted to use, but I am still geting the "Could not find a proper state to initialise" error. Do you have any suggestions?

Random number seed: 1421278847965

File: test3.xml seed: 1421278847965 threads: 1

Probing: beast.jar Skip loading file:/Applications/BEAST 2.1.3/lib/beast.jar: contains classs beast.app.BEASTVersion that is already loaded

Probing: beast.src.jar Loaded URL file:/Applications/BEAST 2.1.3/lib/beast.src.jar

Probing: BEAST_CLASSIC.addon.jar Loaded URL file:/Users/catherinecollins/Library/Application Support/BEAST/2.1/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar

Probing: BEASTlabs.addon.jar Loaded URL file:/Users/catherinecollins/Library/Application Support/BEAST/2.1/BEASTlabs/lib/BEASTlabs.addon.jar

Beta => beast.math.distributions.Beta

Exponential => beast.math.distributions.Exponential

InverseGamma => beast.math.distributions.InverseGamma

LogNormal => beast.math.distributions.LogNormalDistributionModel

Gamma => beast.math.distributions.Gamma

Uniform => beast.math.distributions.Uniform

prior => beast.math.distributions.Prior

LaplaceDistribution => beast.math.distributions.LaplaceDistribution

OneOnX => beast.math.distributions.OneOnX

Normal => beast.math.distributions.Normal

Element data found with idref='converted_TCS'. All other attributes are ignored.

Element parameter found with idref='clockRate.c:converted_TCS'. All other attributes are ignored.

Element tree found with idref='Tree.t:converted_TCS'. All other attributes are ignored.

Element parameter found with idref='popSize.t:converted_TCS'. All other attributes are ignored.

Element parameter found with idref='relativeGeoRates.s:locations'. All other attributes are ignored.

Element parameter found with idref='traitClockRate.c:locations'. All other attributes are ignored.

Element parameter found with idref='clockRate.c:converted_TCS'. All other attributes are ignored.

Element parameter found with idref='kappa.s:converted_TCS'. All other attributes are ignored.

Element parameter found with idref='gammaShape.s:converted_TCS'. All other attributes are ignored.

1037 taxa

524 sites

103 patterns

Starting frequencies: [0.23268088364115513, 0.13464412169573123, 0.1835410424963378, 0.4491339521667759]

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU

  Ignoring ambiguities in tree likelihood.

  With 103 unique site patterns.

  Using rescaling scheme : dynamic

Bs1_JPN1_UN_JPN = JPN (NaN)

Bs2_UN_WDH = WDH (NaN)

Bs3_UN_ALI = ALI (NaN)

Bs4_UN_PLT = PLT (NaN)

Bs5_UN_ALI = ALI (NaN)

Bs6_UN_PLT = PLT (NaN)

Bs7_UN_PLT = PLT (NaN)

Bs8_UN_CI = CI (NaN)

Bs9_UN_ALI = ALI (NaN)

Bs10_JPN11_UN_JPN = JPN (NaN)

Bs12_UN_BRE = BRE (NaN)

Bs13_UN_P3 = P3 (NaN)

Bs14_UN_M3 = M3 (NaN)

Bs15_UN_P3 = P3 (NaN)

Bs16_UN_P5 = P5 (NaN)

Bs22_UN_VEN = VEN (NaN)

Bs23_UN_VEN = VEN (NaN)

Bs24_UN_VEN = VEN (NaN)

Bs25SLJ_UN_VEN = VEN (NaN)

Bs26_UN_VEN = VEN (NaN)

Bs27_UN_CER = CER (NaN)

Bs28_UN_PAL = PAL (NaN)

Bs29_UN_CER = CER (NaN)

Bs30_UN_PAL = PAL (NaN)

Bs32_UN_BRI = BRI (NaN)

Bs36_JPN8_UN_JPN = JPN (NaN)

HASLJ_UN_VEN = VEN (NaN)

HG_legentil_UN_CER = CER (NaN)

HJ_UN_GRANA = GRANA (NaN)

HK_UN_CUB = CUB (NaN)

HO_BR39_UN_BR = BR (NaN)

HP_Lenentil_UN_ETQ = ETQ (NaN)

HD_UN_BRE = BRE (NaN)

HBSLJ_UN_FAL = FAL (NaN)

BR1_UN_BR = BR (NaN)

BR22_UN_BR = BR (NaN)

BR25_UN_BR = BR (NaN)

BR3_UN_BR = BR (NaN)

BR30_UN_BR = BR (NaN)

BR32_UN_BR = BR (NaN)

BR35_UN_BR = BR (NaN)

BR5_UN_BR = BR (NaN)

BR7_UN_BR = BR (NaN)

CI10_UN_CI = CI (NaN)

CI20_UN_CI = CI (NaN)

CI25_UN_CI = CI (NaN)

CI3_UN_CI = CI (NaN)

CI40_UN_CI = CI (NaN)

CI6_UN_CI = CI (NaN)

CI60_UN_CI = CI (NaN)

CI70_UN_CI = CI (NaN)

CT1_UN_CT = CT (NaN)

CT10_UN_CT = CT (NaN)

CT11_UN_CT = CT (NaN)

CT12_UN_CT = CT (NaN)

CT2_UN_CT = CT (NaN)

CT3_UN_CT = CT (NaN)

CT4_UN_CT = CT (NaN)

CT5_UN_CT = CT (NaN)

CT6_UN_CT = CT (NaN)

CT7_UN_CT = CT (NaN)

FAH2_UN_FAL = FAL (NaN)

FAH3_UN_FAL = FAL (NaN)

FAH4_UN_FAL = FAL (NaN)

FAH6_UN_FAL = FAL (NaN)

FAH9_UN_FAL = FAL (NaN)

GL10_UN_GL = GL (NaN)

GL15_UN_GL = GL (NaN)

GL2_UN_GL = GL (NaN)

GL20_UN_GL = GL (NaN)

GL24_UN_GL = GL (NaN)

GL30_UN_GL = GL (NaN)

GL35_UN_GL = GL (NaN)

GL42_UN_GL = GL (NaN)

GL44_UN_GL = GL (NaN)

GL5_UN_GL = GL (NaN)

IRL11_UN_IRL = IRL (NaN)

IRL18_UN_IRL = IRL (NaN)

IRL21_UN_IRL = IRL (NaN)

IRL23_UN_IRL = IRL (NaN)

IRL26_UN_IRL = IRL (NaN)

IRL29_UN_IRL = IRL (NaN)

IRL30_UN_IRL = IRL (NaN)

ITA10SLJ_UN_VEN = VEN (NaN)

ITA4SLJ_UN_VEN = VEN (NaN)

ITA6SLJ_UN_VEN = VEN (NaN)

ITA7SLJ_UN_VEN = VEN (NaN)

ITA8SLJ_UN_VEN = VEN (NaN)

ITA9SLJ_UN_VEN = VEN (NaN)

Jpn10_UN_JPN = JPN (NaN)

Jpn12_UN_JPN = JPN (NaN)

Jpn2_UN_JPN = JPN (NaN)

Jpn3_UN_JPN = JPN (NaN)

Jpn4_UN_JPN = JPN (NaN)

Jpn5_UN_JPN = JPN (NaN)

Jpn6_UN_JPN = JPN (NaN)

Jpn7_UN_JPN = JPN (NaN)

MB1_UN_MB = MB (NaN)

MB22_UN_MB = MB (NaN)

MB3_UN_MB = MB (NaN)

MB30_UN_MB = MB (NaN)

SJ1_UN_MB = MB (NaN)

MB7_UN_MB = MB (NaN)

MHB21_UN_MHB = MHB (NaN)

MHB25_UN_MHB = MHB (NaN)

MHB34_UN_MHB = MHB (NaN)

MHB38_UN_MHB = MHB (NaN)

MHB42_UN_MHB = MHB (NaN)

MHB5_UN_MHB = MHB (NaN)

MHB50_UN_MHB = MHB (NaN)

MHB51_UN_MHB = MHB (NaN)

MHB53_UN_MHB = MHB (NaN)

MHB9_UN_MHB = MHB (NaN)

NethA_UN_NET = NET (NaN)

NethB_UN_NET = NET (NaN)

NethC_UN_NET = NET (NaN)

NethE_UN_NET = NET (NaN)

NethF_UN_NET = NET (NaN)

NethH_UN_NET = NET (NaN)

NethI_UN_NET = NET (NaN)

NH1_UN_NAH = NAH (NaN)

NH10_UN_NAH = NAH (NaN)

NH2_UN_NAH = NAH (NaN)

NH3_UN_NAH = NAH (NaN)

NH4_UN_NAH = NAH (NaN)

NH5_UN_NAH = NAH (NaN)

NH6_UN_NAH = NAH (NaN)

NH8_UN_NAH = NAH (NaN)

NH9_UN_NAH = NAH (NaN)

OP10_UN_OP = OP (NaN)

OP11_UN_OP = OP (NaN)

OP12_UN_OP = OP (NaN)

OP15_UN_OP = OP (NaN)

OP26_UN_OP = OP (NaN)

OP40_UN_OP = OP (NaN)

OP48_UN_OP = OP (NaN)

OP49_UN_OP = OP (NaN)

OP5_UN_OP = OP (NaN)

OP55_UN_OP = OP (NaN)

PEI2_UN_PEI = PEI (NaN)

PEI3_UN_PEI = PEI (NaN)

PEI5_UN_PEI = PEI (NaN)

PEI6_UN_PEI = PEI (NaN)

PEI9_UN_PEI = PEI (NaN)

PP22_UN_PP = PP (NaN)

PP34_UN_PP = PP (NaN)

PP6_UN_PP = PP (NaN)

PP9_UN_PP = PP (NaN)

SB1_UN_SB = SB (NaN)

SB10_UN_SB = SB (NaN)

SB13_UN_SB = SB (NaN)

SB15_UN_SB = SB (NaN)

SB17_UN_SB = SB (NaN)

SB20_UN_SB = SB (NaN)

SB25_UN_SB = SB (NaN)

SB29_UN_SB = SB (NaN)

SB36_UN_SB = SB (NaN)

SB9_UN_SB = SB (NaN)

SFB2_UN_SFB = SFB (NaN)

SFB3B_UN_SFB = SFB (NaN)

SMB14_UN_SMB = SMB (NaN)

SMB17_UN_SMB = SMB (NaN)

SMB2_UN_SMB = SMB (NaN)

SMB20_UN_SMB = SMB (NaN)

SMB28_UN_SMB = SMB (NaN)

SMB33_UN_SMB = SMB (NaN)

SMB37_UN_SMB = SMB (NaN)

SMB42_UN_SMB = SMB (NaN)

SMB61_UN_SMB = SMB (NaN)

SMB7_UN_SMB = SMB (NaN)

WDH11_UN_WDH = WDH (NaN)

WDH20_UN_WDH = WDH (NaN)

WDH25_UN_WDH = WDH (NaN)

WDH26_UN_WDH = WDH (NaN)

WDH35_UN_WDH = WDH (NaN)

WDH4_UN_WDH = WDH (NaN)

WDH40_UN_WDH = WDH (NaN)

WDH41_UN_WDH = WDH (NaN)

WDH46_UN_WDH = WDH (NaN)

BS02NZ_UN_NZN = NZN (NaN)

BS03NZ_UN_NZN = NZN (NaN)

BS04NZ_UN_NZN = NZN (NaN)

BS05NZ_UN_NZN = NZN (NaN)

BS06NZ_UN_NZN = NZN (NaN)

BS07NZ_UN_NZN = NZN (NaN)

BS08NZ_UN_NZN = NZN (NaN)

BS09NZ_UN_NZN = NZN (NaN)

BS10NZ_UN_NZN = NZN (NaN)

BS11NZ_UN_NZN = NZN (NaN)

BS12NZ_UN_NZN = NZN (NaN)

BS13NZ_UN_NZN = NZN (NaN)

BS14NZ_UN_NZN = NZN (NaN)

BS15NZ_UN_NZN = NZN (NaN)

BS16NZ_UN_NZN = NZN (NaN)

PLA1_UN_PLA = PLA (NaN)

PLA2_UN_PLA = PLA (NaN)

PLA3_UN_PLA = PLA (NaN)

JPNLej1_UN_JPN = JPN (NaN)

JPNLej2_UN_JPN = JPN (NaN)

JPNLej3_UN_JPN = JPN (NaN)

P3Lej1_UN_P3 = P3 (NaN)

P3Lej2_UN_P3 = P3 (NaN)

P3Lej3_UN_P3 = P3 (NaN)

P3Lej4_UN_P3 = P3 (NaN)

P3Lej5_UN_P3 = P3 (NaN)

P3Lej6_UN_P3 = P3 (NaN)

P3Lej7_UN_P3 = P3 (NaN)

P3Lej8_UN_P3 = P3 (NaN)

P3Lej9_UN_P3 = P3 (NaN)

P3Lej10_UN_P3 = P3 (NaN)

P3Lej11_UN_P3 = P3 (NaN)

P3Lej12_UN_P3 = P3 (NaN)

P3Lej13_UN_P3 = P3 (NaN)

P3Lej14_UN_P3 = P3 (NaN)

P3Lej15_UN_P3 = P3 (NaN)

P3Lej16_UN_P3 = P3 (NaN)

ADM01_UN_ADM = ADM (NaN)

ADM02_UN_ADM = ADM (NaN)

ADM03_UN_ADM = ADM (NaN)

ADM04_UN_ADM = ADM (NaN)

ADM05_UN_ADM = ADM (NaN)

ADM06_UN_ADM = ADM (NaN)

ADM07_UN_ADM = ADM (NaN)

ADM08_UN_ADM = ADM (NaN)

ADM09_UN_ADM = ADM (NaN)

ADM10_UN_ADM = ADM (NaN)

ADM11_UN_ADM = ADM (NaN)

ADM12_UN_ADM = ADM (NaN)

ADM13_UN_ADM = ADM (NaN)

ADM14_UN_ADM = ADM (NaN)

ADM15_UN_ADM = ADM (NaN)

ADM16_UN_ADM = ADM (NaN)

ADM17_UN_ADM = ADM (NaN)

ADM18_UN_ADM = ADM (NaN)

ADM19_UN_ADM = ADM (NaN)

ADM20_UN_ADM = ADM (NaN)

ADM21_UN_ADM = ADM (NaN)

ADM22_UN_ADM = ADM (NaN)

ADM23_UN_ADM = ADM (NaN)

ADM24_UN_ADM = ADM (NaN)

ADM25_UN_ADM = ADM (NaN)

ADM26_UN_ADM = ADM (NaN)

ADM27_UN_ADM = ADM (NaN)

ADM28_UN_ADM = ADM (NaN)

ADM29_UN_ADM = ADM (NaN)

ADM30_UN_ADM = ADM (NaN)

ADM31_UN_ADM = ADM (NaN)

ADM32_UN_ADM = ADM (NaN)

ADM33_UN_ADM = ADM (NaN)

ADM34_UN_ADM = ADM (NaN)

ADM35_UN_ADM = ADM (NaN)

ADM36_UN_ADM = ADM (NaN)

ALI01_UN_ALI = ALI (NaN)

ALI02_UN_ALI = ALI (NaN)

ALI03_UN_ALI = ALI (NaN)

ALI04_UN_ALI = ALI (NaN)

ALI06_UN_ALI = ALI (NaN)

ALI07_UN_ALI = ALI (NaN)

ALI08_UN_ALI = ALI (NaN)

ALI09_UN_ALI = ALI (NaN)

ALI10_UN_ALI = ALI (NaN)

ALI11_UN_ALI = ALI (NaN)

ALI12_UN_ALI = ALI (NaN)

ALI13_UN_ALI = ALI (NaN)

ALI14_UN_ALI = ALI (NaN)

ALI15_UN_ALI = ALI (NaN)

ALI16_UN_ALI = ALI (NaN)

ALI17_UN_ALI = ALI (NaN)

ALI19_UN_ALI = ALI (NaN)

ALI20_UN_ALI = ALI (NaN)

ALI21_UN_ALI = ALI (NaN)

ALI22_UN_ALI = ALI (NaN)

ALI23_UN_ALI = ALI (NaN)

ALI24_UN_ALI = ALI (NaN)

ALI25_UN_ALI = ALI (NaN)

ALI27_UN_ALI = ALI (NaN)

ALI28_UN_ALI = ALI (NaN)

BBY01_UN_BBY = BBY (NaN)

BBY02_UN_BBY = BBY (NaN)

BBY03_UN_BBY = BBY (NaN)

BBY04_UN_BBY = BBY (NaN)

BBY05_UN_BBY = BBY (NaN)

BBY06_UN_BBY = BBY (NaN)

BBY07_UN_BBY = BBY (NaN)

BBY08_UN_BBY = BBY (NaN)

BBY09_UN_BBY = BBY (NaN)

BBY10_UN_BBY = BBY (NaN)

BBY11_UN_BBY = BBY (NaN)

BBY12_UN_BBY = BBY (NaN)

BBY13_UN_BBY = BBY (NaN)

BBY14_UN_BBY = BBY (NaN)

BBY15_UN_BBY = BBY (NaN)

BBY16_UN_BBY = BBY (NaN)

BBY17_UN_BBY = BBY (NaN)

BBY18_UN_BBY = BBY (NaN)

BBY19_UN_BBY = BBY (NaN)

BBY20_UN_BBY = BBY (NaN)

BBY21_UN_BBY = BBY (NaN)

BBY22_UN_BBY = BBY (NaN)

BBY23_UN_BBY = BBY (NaN)

BBY24_UN_BBY = BBY (NaN)

BBY25_UN_BBY = BBY (NaN)

BBY26_UN_BBY = BBY (NaN)

BBY27_UN_BBY = BBY (NaN)

BBY28_UN_BBY = BBY (NaN)

BBY29_UN_BBY = BBY (NaN)

BBY30_UN_BBY = BBY (NaN)

BBY31_UN_BBY = BBY (NaN)

BBY32_UN_BBY = BBY (NaN)

BBY33_UN_BBY = BBY (NaN)

BBY34_UN_BBY = BBY (NaN)

BBY35_UN_BBY = BBY (NaN)

BBY36_UN_BBY = BBY (NaN)

BLA01_UN_BLA = BLA (NaN)

BLA02_UN_BLA = BLA (NaN)

BLA03_UN_BLA = BLA (NaN)

BLA04_UN_BLA = BLA (NaN)

BLA05_UN_BLA = BLA (NaN)

BLA06_UN_BLA = BLA (NaN)

BLA07_UN_BLA = BLA (NaN)

BLA08_UN_BLA = BLA (NaN)

BLA09_UN_BLA = BLA (NaN)

BLA10_UN_BLA = BLA (NaN)

BLA11_UN_BLA = BLA (NaN)

BLA12_UN_BLA = BLA (NaN)

BLA13_UN_BLA = BLA (NaN)

BLA14_UN_BLA = BLA (NaN)

BLA15_UN_BLA = BLA (NaN)

BLA16_UN_BLA = BLA (NaN)

BLA17_UN_BLA = BLA (NaN)

BLA18_UN_BLA = BLA (NaN)

BLA19_UN_BLA = BLA (NaN)

BLA20_UN_BLA = BLA (NaN)

BLA21_UN_BLA = BLA (NaN)

BLA22_UN_BLA = BLA (NaN)

BLA23_UN_BLA = BLA (NaN)

BLA24_UN_BLA = BLA (NaN)

BRE02_UN_BRE = BRE (NaN)

BRE03_UN_BRE = BRE (NaN)

BRE04_UN_BRE = BRE (NaN)

BRE06_UN_BRE = BRE (NaN)

BRE07_UN_BRE = BRE (NaN)

BRE08_UN_BRE = BRE (NaN)

BRE09_UN_BRE = BRE (NaN)

BRE10_UN_BRE = BRE (NaN)

BRE11_UN_BRE = BRE (NaN)

BRE12_UN_BRE = BRE (NaN)

BRE14_UN_BRE = BRE (NaN)

BRE15_UN_BRE = BRE (NaN)

BRE16_UN_BRE = BRE (NaN)

BRE17_UN_BRE = BRE (NaN)

BRE18_UN_BRE = BRE (NaN)

BRE19_UN_BRE = BRE (NaN)

BRE20_UN_BRE = BRE (NaN)

BRE21_UN_BRE = BRE (NaN)

BRE22_UN_BRE = BRE (NaN)

BRE23_UN_BRE = BRE (NaN)

BRE24_UN_BRE = BRE (NaN)

BRE25_UN_BRE = BRE (NaN)

BRE26_UN_BRE = BRE (NaN)

BRE27_UN_BRE = BRE (NaN)

BRE28_UN_BRE = BRE (NaN)

BRE29_UN_BRE = BRE (NaN)

BRE30_UN_BRE = BRE (NaN)

BRE31_UN_BRE = BRE (NaN)

BRE32_UN_BRE = BRE (NaN)

BRE33_UN_BRE = BRE (NaN)

BRE34_UN_BRE = BRE (NaN)

BRE35_UN_BRE = BRE (NaN)

BRE36_UN_BRE = BRE (NaN)

BRE37_UN_BRE = BRE (NaN)

BRI01_UN_BRI = BRI (NaN)

BRI03_UN_BRI = BRI (NaN)

BRI04_UN_BRI = BRI (NaN)

BRI05_UN_BRI = BRI (NaN)

BRI06_UN_BRI = BRI (NaN)

BRI07_UN_BRI = BRI (NaN)

BRI08_UN_BRI = BRI (NaN)

BRI09_UN_BRI = BRI (NaN)

BRI11_UN_BRI = BRI (NaN)

BRI12_UN_BRI = BRI (NaN)

BRI13_UN_BRI = BRI (NaN)

BRI14_UN_BRI = BRI (NaN)

BRI15_UN_BRI = BRI (NaN)

BRI16_UN_BRI = BRI (NaN)

BRI17_UN_BRI = BRI (NaN)

BRI18_UN_BRI = BRI (NaN)

BRI19_UN_BRI = BRI (NaN)

BRI20_UN_BRI = BRI (NaN)

BRI21_UN_BRI = BRI (NaN)

BRN01_UN_BRN = BRN (NaN)

BRN02_UN_BRN = BRN (NaN)

BRN03_UN_BRN = BRN (NaN)

BRN04_UN_BRN = BRN (NaN)

BRN05_UN_BRN = BRN (NaN)

BRN06_UN_BRN = BRN (NaN)

BRN07_UN_BRN = BRN (NaN)

BRN08_UN_BRN = BRN (NaN)

BRN09_UN_BRN = BRN (NaN)

BRN10_UN_BRN = BRN (NaN)

BRN11_UN_BRN = BRN (NaN)

CER01_UN_CER = CER (NaN)

CER02_UN_CER = CER (NaN)

CER03_UN_CER = CER (NaN)

CER04_UN_CER = CER (NaN)

CER05_UN_CER = CER (NaN)

CER06_UN_CER = CER (NaN)

CER07_UN_CER = CER (NaN)

CER08_UN_CER = CER (NaN)

CER09_UN_CER = CER (NaN)

CER10_UN_CER = CER (NaN)

CER11_UN_CER = CER (NaN)

CER13_UN_CER = CER (NaN)

CER14_UN_CER = CER (NaN)

CER15_UN_CER = CER (NaN)

CER16_UN_CER = CER (NaN)

CER17_UN_CER = CER (NaN)

CER18_UN_CER = CER (NaN)

CER20_UN_CER = CER (NaN)

CER21_UN_CER = CER (NaN)

CER22_UN_CER = CER (NaN)

CER23_UN_CER = CER (NaN)

CER24_UN_CER = CER (NaN)

CER25_UN_CER = CER (NaN)

CER26_UN_CER = CER (NaN)

CER27_UN_CER = CER (NaN)

CER28_UN_CER = CER (NaN)

CER29_UN_CER = CER (NaN)

CER30_UN_CER = CER (NaN)

CER31_UN_CER = CER (NaN)

CER32_UN_CER = CER (NaN)

CER33_UN_CER = CER (NaN)

CER34_UN_CER = CER (NaN)

CER35_UN_CER = CER (NaN)

CER36_UN_CER = CER (NaN)

DGB01_UN_DGB = DGB (NaN)

DGB02_UN_DGB = DGB (NaN)

DGB03_UN_DGB = DGB (NaN)

DGB04_UN_DGB = DGB (NaN)

DGB05_UN_DGB = DGB (NaN)

DGB06_UN_DGB = DGB (NaN)

DPB01_UN_DPB = DPB (NaN)

DPB02_UN_DPB = DPB (NaN)

DPB03_UN_DPB = DPB (NaN)

DPB04_UN_DPB = DPB (NaN)

DPB05_UN_DPB = DPB (NaN)

DPB06_UN_DPB = DPB (NaN)

DPB07_UN_DPB = DPB (NaN)

DPB08_UN_DPB = DPB (NaN)

DPB09_UN_DPB = DPB (NaN)

ETQ01_UN_ETQ = ETQ (NaN)

ETQ02_UN_ETQ = ETQ (NaN)

ETQ03_UN_ETQ = ETQ (NaN)

ETQ04_UN_ETQ = ETQ (NaN)

ETQ05_UN_ETQ = ETQ (NaN)

ETQ06_UN_ETQ = ETQ (NaN)

ETQ07_UN_ETQ = ETQ (NaN)

ETQ08_UN_ETQ = ETQ (NaN)

ETQ09_UN_ETQ = ETQ (NaN)

ETQ10_UN_ETQ = ETQ (NaN)

ETQ11_UN_ETQ = ETQ (NaN)

FAL01_UN_FAL = FAL (NaN)

FAL02_UN_FAL = FAL (NaN)

FAL03_UN_FAL = FAL (NaN)

FAL04_UN_FAL = FAL (NaN)

FAL05_UN_FAL = FAL (NaN)

FAL06_UN_FAL = FAL (NaN)

FAL07_UN_FAL = FAL (NaN)

FAL08_UN_FAL = FAL (NaN)

FAL09_UN_FAL = FAL (NaN)

FAL10_UN_FAL = FAL (NaN)

FAL11_UN_FAL = FAL (NaN)

FAL12_UN_FAL = FAL (NaN)

FAL13_UN_FAL = FAL (NaN)

FAL14_UN_FAL = FAL (NaN)

FAL15_UN_FAL = FAL (NaN)

FAL16_UN_FAL = FAL (NaN)

FAL17_UN_FAL = FAL (NaN)

FAL18_UN_FAL = FAL (NaN)

FAL19_UN_FAL = FAL (NaN)

FAL20_UN_FAL = FAL (NaN)

FAL21_UN_FAL = FAL (NaN)

FAL22_UN_FAL = FAL (NaN)

FAL23_UN_FAL = FAL (NaN)

FAL24_UN_FAL = FAL (NaN)

FAL25_UN_FAL = FAL (NaN)

FAL26_UN_FAL = FAL (NaN)

FAL27_UN_FAL = FAL (NaN)

FAL28_UN_FAL = FAL (NaN)

FAL29_UN_FAL = FAL (NaN)

FAL30_UN_FAL = FAL (NaN)

FAL31_UN_FAL = FAL (NaN)

FAL32_UN_FAL = FAL (NaN)

FAL33_UN_FAL = FAL (NaN)

FAL34_UN_FAL = FAL (NaN)

FAL35_UN_FAL = FAL (NaN)

FAL36_UN_FAL = FAL (NaN)

FAL37_UN_FAL = FAL (NaN)

FAL38_UN_FAL = FAL (NaN)

FAL39_UN_FAL = FAL (NaN)

FAL40_UN_FAL = FAL (NaN)

FAL41_UN_FAL = FAL (NaN)

FAL42_UN_FAL = FAL (NaN)

FAL43_UN_FAL = FAL (NaN)

FRC01_UN_FRC = FRC (NaN)

FRC02_UN_FRC = FRC (NaN)

FRC03_UN_FRC = FRC (NaN)

FRC04_UN_FRC = FRC (NaN)

FRC05_UN_FRC = FRC (NaN)

FRC06_UN_FRC = FRC (NaN)

FRC07_UN_FRC = FRC (NaN)

FRC08_UN_FRC = FRC (NaN)

FRC09_UN_FRC = FRC (NaN)

FRC10_UN_FRC = FRC (NaN)

FRC11_UN_FRC = FRC (NaN)

FRC12_UN_FRC = FRC (NaN)

FRC13_UN_FRC = FRC (NaN)

FRC14_UN_FRC = FRC (NaN)

FRC15_UN_FRC = FRC (NaN)

FRC16_UN_FRC = FRC (NaN)

FRC17_UN_FRC = FRC (NaN)

FRC18_UN_FRC = FRC (NaN)

FRC19_UN_FRC = FRC (NaN)

FRC20_UN_FRC = FRC (NaN)

FRC21_UN_FRC = FRC (NaN)

FRC22_UN_FRC = FRC (NaN)

FRC23_UN_FRC = FRC (NaN)

HEL01_UN_HEL = HEL (NaN)

HEL02_UN_HEL = HEL (NaN)

HEL03_UN_HEL = HEL (NaN)

HEL04_UN_HEL = HEL (NaN)

HEL05_UN_HEL = HEL (NaN)

HEL06_UN_HEL = HEL (NaN)

HEL07_UN_HEL = HEL (NaN)

HEL08_UN_HEL = HEL (NaN)

HEL09_UN_HEL = HEL (NaN)

HEL10_UN_HEL = HEL (NaN)

HEL11_UN_HEL = HEL (NaN)

HEL12_UN_HEL = HEL (NaN)

HEL13_UN_HEL = HEL (NaN)

HEL14_UN_HEL = HEL (NaN)

HEL15_UN_HEL = HEL (NaN)

HEL16_UN_HEL = HEL (NaN)

HEL17_UN_HEL = HEL (NaN)

HEL18_UN_HEL = HEL (NaN)

HEL19_UN_HEL = HEL (NaN)

IGM01_UN_IGM = IGM (NaN)

IGM02_UN_IGM = IGM (NaN)

IGM03_UN_IGM = IGM (NaN)

IGM04_UN_IGM = IGM (NaN)

IGM05_UN_IGM = IGM (NaN)

IGM06_UN_IGM = IGM (NaN)

IGM07_UN_IGM = IGM (NaN)

IGM08_UN_IGM = IGM (NaN)

LSB01_UN_LSB = LSB (NaN)

LSB02_UN_LSB = LSB (NaN)

LSM01_UN_LSM = LSM (NaN)

LSM02_UN_LSM = LSM (NaN)

LSM03_UN_LSM = LSM (NaN)

LSM04_UN_LSM = LSM (NaN)

LSM05_UN_LSM = LSM (NaN)

LSM06_UN_LSM = LSM (NaN)

LSM07_UN_LSM = LSM (NaN)

LSM08_UN_LSM = LSM (NaN)

LSM09_UN_LSM = LSM (NaN)

LSM10_UN_LSM = LSM (NaN)

LSM11_UN_LSM = LSM (NaN)

LSM12_UN_LSM = LSM (NaN)

LSM13_UN_LSM = LSM (NaN)

LSM14_UN_LSM = LSM (NaN)

LSM15_UN_LSM = LSM (NaN)

NAP01_UN_NAP = NAP (NaN)

NAP02_UN_NAP = NAP (NaN)

NAP03_UN_NAP = NAP (NaN)

NAP04_UN_NAP = NAP (NaN)

NAP05_UN_NAP = NAP (NaN)

NAP06_UN_NAP = NAP (NaN)

NAP07_UN_NAP = NAP (NaN)

PAL01_UN_PAL = PAL (NaN)

PAL02_UN_PAL = PAL (NaN)

PAL03_UN_PAL = PAL (NaN)

PAL04_UN_PAL = PAL (NaN)

PAL05_UN_PAL = PAL (NaN)

PAL06_UN_PAL = PAL (NaN)

PAL07_UN_PAL = PAL (NaN)

PAL08_UN_PAL = PAL (NaN)

PAL09_UN_PAL = PAL (NaN)

PAL10_UN_PAL = PAL (NaN)

PAL11_UN_PAL = PAL (NaN)

PAL12_UN_PAL = PAL (NaN)

PAL14_UN_PAL = PAL (NaN)

PAL15_UN_PAL = PAL (NaN)

PAL16_UN_PAL = PAL (NaN)

PAL17_UN_PAL = PAL (NaN)

PAL18_UN_PAL = PAL (NaN)

PEN01_UN_PEN = PEN (NaN)

PEN02_UN_PEN = PEN (NaN)

PEN03_UN_PEN = PEN (NaN)

PEN04_UN_PEN = PEN (NaN)

PEN05_UN_PEN = PEN (NaN)

PEN06_UN_PEN = PEN (NaN)

PEN07_UN_PEN = PEN (NaN)

PEN08_UN_PEN = PEN (NaN)

PEN09_UN_PEN = PEN (NaN)

PEN10_UN_PEN = PEN (NaN)

PEN11_UN_PEN = PEN (NaN)

PEN12_UN_PEN = PEN (NaN)

PEN13_UN_PEN = PEN (NaN)

PEN14_UN_PEN = PEN (NaN)

PEN15_UN_PEN = PEN (NaN)

PEN16_UN_PEN = PEN (NaN)

PEN17_UN_PEN = PEN (NaN)

PEN18_UN_PEN = PEN (NaN)

PLT01_UN_PLT = PLT (NaN)

PLT02_UN_PLT = PLT (NaN)

PLT03_UN_PLT = PLT (NaN)

PLT05_UN_PLT = PLT (NaN)

PLT06_UN_PLT = PLT (NaN)

PLT07_UN_PLT = PLT (NaN)

PLT08_UN_PLT = PLT (NaN)

PLT10_UN_PLT = PLT (NaN)

PLY01_UN_PLY = PLY (NaN)

PLY02_UN_PLY = PLY (NaN)

PLY03_UN_PLY = PLY (NaN)

PLY04_UN_PLY = PLY (NaN)

PLY05_UN_PLY = PLY (NaN)

PLY06_UN_PLY = PLY (NaN)

PLY07_UN_PLY = PLY (NaN)

PLY08_UN_PLY = PLY (NaN)

PLY09_UN_PLY = PLY (NaN)

PLY10_UN_PLY = PLY (NaN)

PLY11_UN_PLY = PLY (NaN)

PLY12_UN_PLY = PLY (NaN)

PLY13_UN_PLY = PLY (NaN)

PLY14_UN_PLY = PLY (NaN)

PLY15_UN_PLY = PLY (NaN)

PLY16_UN_PLY = PLY (NaN)

PLY17_UN_PLY = PLY (NaN)

PLY18_UN_PLY = PLY (NaN)

PLY19_UN_PLY = PLY (NaN)

PLY21_UN_PLY = PLY (NaN)

PLY22_UN_PLY = PLY (NaN)

PLY23_UN_PLY = PLY (NaN)

PLY24_UN_PLY = PLY (NaN)

PLY25_UN_PLY = PLY (NaN)

PLY26_UN_PLY = PLY (NaN)

PLY27_UN_PLY = PLY (NaN)

PLY28_UN_PLY = PLY (NaN)

PLY29_UN_PLY = PLY (NaN)

PLY30_UN_PLY = PLY (NaN)

PLY32_UN_PLY = PLY (NaN)

PLY33_UN_PLY = PLY (NaN)

PLY34_UN_PLY = PLY (NaN)

RCF02_UN_RCF = RCF (NaN)

RCF03_UN_RCF = RCF (NaN)

RCF04_UN_RCF = RCF (NaN)

RCF05_UN_RCF = RCF (NaN)

RCF06_UN_RCF = RCF (NaN)

RCF07_UN_RCF = RCF (NaN)

RCF08_UN_RCF = RCF (NaN)

RCF09_UN_RCF = RCF (NaN)

RCF10_UN_RCF = RCF (NaN)

RCF11_UN_RCF = RCF (NaN)

RCF12_UN_RCF = RCF (NaN)

RCF13_UN_RCF = RCF (NaN)

RCF14_UN_RCF = RCF (NaN)

RCF15_UN_RCF = RCF (NaN)

RCF16_UN_RCF = RCF (NaN)

RCF17_UN_RCF = RCF (NaN)

RCF18_UN_RCF = RCF (NaN)

RCF19_UN_RCF = RCF (NaN)

RCF20_UN_RCF = RCF (NaN)

RCF21_UN_RCF = RCF (NaN)

RCF22_UN_RCF = RCF (NaN)

RCF23_UN_RCF = RCF (NaN)

RCF24_UN_RCF = RCF (NaN)

RCF25_UN_RCF = RCF (NaN)

RCF26_UN_RCF = RCF (NaN)

RCF27_UN_RCF = RCF (NaN)

RCF28_UN_RCF = RCF (NaN)

RCF29_UN_RCF = RCF (NaN)

RCF30_UN_RCF = RCF (NaN)

RCF31_UN_RCF = RCF (NaN)

RCF32_UN_RCF = RCF (NaN)

RCF33_UN_RCF = RCF (NaN)

RCF34_UN_RCF = RCF (NaN)

RCF35_UN_RCF = RCF (NaN)

SAL01_UN_SAL = SAL (NaN)

SAL02_UN_SAL = SAL (NaN)

SAL03_UN_SAL = SAL (NaN)

SAL04_UN_SAL = SAL (NaN)

SAL05_UN_SAL = SAL (NaN)

SAL06_UN_SAL = SAL (NaN)

SAL07_UN_SAL = SAL (NaN)

SAL08_UN_SAL = SAL (NaN)

SAL09_UN_SAL = SAL (NaN)

SAL10_UN_SAL = SAL (NaN)

SET01_UN_SET = SET (NaN)

SET02_UN_SET = SET (NaN)

SET04_UN_SET = SET (NaN)

SET05_UN_SET = SET (NaN)

SET06_UN_SET = SET (NaN)

SQM01_UN_SQM = SQM (NaN)

SQM02_UN_SQM = SQM (NaN)

SQM03_UN_SQM = SQM (NaN)

SQM04_UN_SQM = SQM (NaN)

SQM05_UN_SQM = SQM (NaN)

SQM06_UN_SQM = SQM (NaN)

STP01_UN_STP = STP (NaN)

STP02_UN_STP = STP (NaN)

STP03_UN_STP = STP (NaN)

STP04_UN_STP = STP (NaN)

STP05_UN_STP = STP (NaN)

TOR01_UN_TOR = TOR (NaN)

TOR02_UN_TOR = TOR (NaN)

TOR03_UN_TOR = TOR (NaN)

TOR04_UN_TOR = TOR (NaN)

VEN01_UN_VEN = VEN (NaN)

VEN02_UN_VEN = VEN (NaN)

VEN03_UN_VEN = VEN (NaN)

VEN04_UN_VEN = VEN (NaN)

VEN05_UN_VEN = VEN (NaN)

VEN06_UN_VEN = VEN (NaN)

VEN08_UN_VEN = VEN (NaN)

VEN10_UN_VEN = VEN (NaN)

VEN11_UN_VEN = VEN (NaN)

VEN12_UN_VEN = VEN (NaN)

VEN13_UN_VEN = VEN (NaN)

VEN14_UN_VEN = VEN (NaN)

VEN16_UN_VEN = VEN (NaN)

VEN17_UN_VEN = VEN (NaN)

VEN18_UN_VEN = VEN (NaN)

VEN20_UN_VEN = VEN (NaN)

VEN21_UN_VEN = VEN (NaN)

VEN22_UN_VEN = VEN (NaN)

VEN23_UN_VEN = VEN (NaN)

VEN24_UN_VEN = VEN (NaN)

VEN25_UN_VEN = VEN (NaN)

VEN26_UN_VEN = VEN (NaN)

VEN27_UN_VEN = VEN (NaN)

VEN28_UN_VEN = VEN (NaN)

WDH01_UN_WDH = WDH (NaN)

WDH02_UN_WDH = WDH (NaN)

WDH03_UN_WDH = WDH (NaN)

WDH04_UN_WDH = WDH (NaN)

WDH05_UN_WDH = WDH (NaN)

WDH06_UN_WDH = WDH (NaN)

WDH07_UN_WDH = WDH (NaN)

WDH08_UN_WDH = WDH (NaN)

WDH09_UN_WDH = WDH (NaN)

WDH10_UN_WDH = WDH (NaN)

WDH11_UN_W_0 = 0 (0.0)

WDH12_UN_WDH = WDH (NaN)

WDH13_UN_WDH = WDH (NaN)

EstartitHA1_UN_EST = EST (NaN)

EstartitHA2_UN_EST = EST (NaN)

EstartitHA3_UN_EST = EST (NaN)

EstartitHA4_UN_EST = EST (NaN)

EstartitHA5_UN_EST = EST (NaN)

EstartitHA6_UN_EST = EST (NaN)

EstartitHA7_UN_EST = EST (NaN)

EstartitHB1_UN_EST = EST (NaN)

EstartitHB2_UN_EST = EST (NaN)

EstartitHB3_UN_EST = EST (NaN)

EstartitHB4_UN_EST = EST (NaN)

EstartitHB5_UN_EST = EST (NaN)

EstartitHB6_UN_EST = EST (NaN)

EstartitHB7_UN_EST = EST (NaN)

EstartitHB8_UN_EST = EST (NaN)

EstartitHB9_UN_EST = EST (NaN)

RosesHA1_UN_ROS = ROS (NaN)

RosesHA2_UN_ROS = ROS (NaN)

RosesHA3_UN_ROS = ROS (NaN)

RosesHA4_UN_ROS = ROS (NaN)

RosesHA5_UN_ROS = ROS (NaN)

RosesHA6_UN_ROS = ROS (NaN)

RosesHA7_UN_ROS = ROS (NaN)

RosesHA8_UN_ROS = ROS (NaN)

RosesHF2_UN_ROS = ROS (NaN)

CanetHA1_UN_CER = CER (NaN)

CanetHA2_UN_CER = CER (NaN)

CanetHA3_UN_CER = CER (NaN)

CanetHA4_UN_CER = CER (NaN)

CanetHF1_UN_CER = CER (NaN)

CanetHF2_UN_CER = CER (NaN)

CanetHF3_UN_CER = CER (NaN)

CanetHF4_UN_CER = CER (NaN)

CanetHF5_UN_CER = CER (NaN)

CanetHF6_UN_CER = CER (NaN)

CanetHF7_UN_CER = CER (NaN)

CanetHG2_UN_CER = CER (NaN)

CanetHG3_UN_CER = CER (NaN)

CanetHG4_UN_CER = CER (NaN)

CubellesHA1_UN_CUB = CUB (NaN)

CubellesHA2_UN_CUB = CUB (NaN)

CubellesHA3_UN_CUB = CUB (NaN)

CubellesHA4_UN_CUB = CUB (NaN)

CubellesHA5_UN_CUB = CUB (NaN)

CubellesHK2_UN_CUB = CUB (NaN)

CubellesHK3_UN_CUB = CUB (NaN)

CubellesHK4_UN_CUB = CUB (NaN)

CubellesHK5_UN_CUB = CUB (NaN)

CubellesHK6_UN_CUB = CUB (NaN)

CubellesHK7_UN_CUB = CUB (NaN)

CubellesHK8_UN_CUB = CUB (NaN)

CubellesHK9_UN_CUB = CUB (NaN)

LaRochelleHB1_UN_LAR = LAR (NaN)

LaRochelleHB2_UN_LAR = LAR (NaN)

LaRochelleHB3_UN_LAR = LAR (NaN)

LaRochelleHB4_UN_LAR = LAR (NaN)

LaRochelleHB5_UN_LAR = LAR (NaN)

LaRochelleHB6_UN_LAR = LAR (NaN)

LaRochelleHB7_UN_LAR = LAR (NaN)

LaRochelleHB8_UN_LAR = LAR (NaN)

LaRochelleHO1_UN_LAR = LAR (NaN)

LaRochelleHO2_UN_LAR = LAR (NaN)

LaRochelleHO3_UN_LAR = LAR (NaN)

LaRochelleHO4_UN_LAR = LAR (NaN)

LaRochelleHO5_UN_LAR = LAR (NaN)

LaRochelleHO6_UN_LAR = LAR (NaN)

LaRochelleHO7_UN_LAR = LAR (NaN)

LaRochelleHO8_UN_LAR = LAR (NaN)

LaRochelleHO9_UN_LAR = LAR (NaN)

LaRochelleHO10_UN_LAR = LAR (NaN)

P131G_UN_P1 = P1 (NaN)

P132.1D32_UN_P1 = P1 (NaN)

P132.2_UN_P1 = P1 (NaN)

P133D33_UN_P1 = P1 (NaN)

P133G3_UN_P1 = P1 (NaN)

P135G_UN_P1 = P1 (NaN)

P136.1D36_UN_P1 = P1 (NaN)

P136.2_UN_P1 = P1 (NaN)

P136.3_UN_P1 = P1 (NaN)

P136G_UN_P1 = P1 (NaN)

P138.1A38_UN_P1 = P1 (NaN)

P138.3_UN_P1 = P1 (NaN)

P138B_UN_P1 = P1 (NaN)

P138G3_UN_P1 = P1 (NaN)

P138G6_UN_P1 = P1 (NaN)

P138G7_UN_P1 = P1 (NaN)

P138G1_UN_P1 = P1 (NaN)

P138G2_UN_P1 = P1 (NaN)

P138G4_UN_P1 = P1 (NaN)

P138G5_UN_P1 = P1 (NaN)

P139.1D39_UN_P1 = P1 (NaN)

P139.2_UN_P1 = P1 (NaN)

P139G_UN_P1 = P1 (NaN)

P131D_UN_P1 = P1 (NaN)

P132G_UN_P1 = P1 (NaN)

P135D_UN_P1 = P1 (NaN)

P138C_UN_P1 = P1 (NaN)

P138D_UN_P1 = P1 (NaN)

P139A_UN_P1 = P1 (NaN)

P225D1_UN_P2 = P2 (NaN)

P225D2_UN_P2 = P2 (NaN)

P226_UN_P2 = P2 (NaN)

P229G1_UN_P2 = P2 (NaN)

P229G2_UN_P2 = P2 (NaN)

P223G_UN_P2 = P2 (NaN)

P224G_UN_P2 = P2 (NaN)

P225G_UN_P2 = P2 (NaN)

P226B_UN_P2 = P2 (NaN)

P461C4_UN_P4 = P4 (NaN)

P461D1_UN_P4 = P4 (NaN)

P461D2_UN_P4 = P4 (NaN)

P461G2_UN_P4 = P4 (NaN)

P463.1_UN_P4 = P4 (NaN)

P463.2_UN_P4 = P4 (NaN)

P464D1_UN_P4 = P4 (NaN)

P464D2_UN_P4 = P4 (NaN)

P466A1_UN_P4 = P4 (NaN)

P466A2_UN_P4 = P4 (NaN)

P466B3_UN_P4 = P4 (NaN)

P466C4_UN_P4 = P4 (NaN)

P466D2_UN_P4 = P4 (NaN)

P466D3_UN_P4 = P4 (NaN)

P466G5_UN_P4 = P4 (NaN)

P466G7_UN_P4 = P4 (NaN)

P467A15_UN_P4 = P4 (NaN)

P467B2_UN_P4 = P4 (NaN)

P467B4_UN_P4 = P4 (NaN)

P467B9_UN_P4 = P4 (NaN)

P467D5_UN_P4 = P4 (NaN)

P467G15_UN_P4 = P4 (NaN)

P467G17_UN_P4 = P4 (NaN)

P467G19_UN_P4 = P4 (NaN)

P467G20_UN_P4 = P4 (NaN)

P467G5_UN_P4 = P4 (NaN)

P467G7_UN_P4 = P4 (NaN)

P468A2_UN_P4 = P4 (NaN)

P468B4_UN_P4 = P4 (NaN)

P468C_UN_P4 = P4 (NaN)

P468C2_UN_P4 = P4 (NaN)

P468D6_UN_P4 = P4 (NaN)

P468G7_UN_P4 = P4 (NaN)

P469A2_UN_P4 = P4 (NaN)

P469D2_UN_P4 = P4 (NaN)

P469D3_UN_P4 = P4 (NaN)

P469G2_UN_P4 = P4 (NaN)

P469G6_UN_P4 = P4 (NaN)

P460A_UN_P4 = P4 (NaN)

P460B_UN_P4 = P4 (NaN)

P460C_UN_P4 = P4 (NaN)

P460D_UN_P4 = P4 (NaN)

P460G_UN_P4 = P4 (NaN)

P461CB61_UN_P4 = P4 (NaN)

P462A_UN_P4 = P4 (NaN)

P462B_UN_P4 = P4 (NaN)

P462C_UN_P4 = P4 (NaN)

P462D_UN_P4 = P4 (NaN)

P462G_UN_P4 = P4 (NaN)

P463A_UN_P4 = P4 (NaN)

P463B_UN_P4 = P4 (NaN)

P463C_UN_P4 = P4 (NaN)

P463G_UN_P4 = P4 (NaN)

P464A_UN_P4 = P4 (NaN)

P464D_UN_P4 = P4 (NaN)

P464G_UN_P4 = P4 (NaN)

P465A_UN_P4 = P4 (NaN)

P465B_UN_P4 = P4 (NaN)

P465D_UN_P4 = P4 (NaN)

P465G_UN_P4 = P4 (NaN)

P467C_UN_P4 = P4 (NaN)

P469B_UN_P4 = P4 (NaN)

P469C_UN_P4 = P4 (NaN)

P551.8B51_UN_P5 = P5 (NaN)

P552C_UN_P5 = P5 (NaN)

P553.1A53_UN_P5 = P5 (NaN)

P553.2D53_UN_P5 = P5 (NaN)

P553.3_UN_P5 = P5 (NaN)

P553.4_UN_P5 = P5 (NaN)

P553B_UN_P5 = P5 (NaN)

P553C_UN_P5 = P5 (NaN)

P553G_UN_P5 = P5 (NaN)

P554.1D54_UN_P5 = P5 (NaN)

P554.2_UN_P5 = P5 (NaN)

P554A1_UN_P5 = P5 (NaN)

P554A3_UN_P5 = P5 (NaN)

P554A2_UN_P5 = P5 (NaN)

P554B_UN_P5 = P5 (NaN)

P554C_UN_P5 = P5 (NaN)

P554C1_UN_P5 = P5 (NaN)

P554G1_UN_P5 = P5 (NaN)

P554G10_UN_P5 = P5 (NaN)

P554G2_UN_P5 = P5 (NaN)

P554G3_UN_P5 = P5 (NaN)

P554G4_UN_P5 = P5 (NaN)

P554G5_UN_P5 = P5 (NaN)

P554G7_UN_P5 = P5 (NaN)

P554G9_UN_P5 = P5 (NaN)

P555.1D55_UN_P5 = P5 (NaN)

P555B_UN_P5 = P5 (NaN)

P555C_UN_P5 = P5 (NaN)

P551A_UN_P5 = P5 (NaN)

M3A1_UN_P3 = P3 (NaN)

M3A10_UN_M3 = M3 (NaN)

M3A2_UN_M3 = M3 (NaN)

M3A3_UN_M3 = M3 (NaN)

M3A4_UN_M3 = M3 (NaN)

M3A5_UN_M3 = M3 (NaN)

M3A6_UN_M3 = M3 (NaN)

M3A7_UN_M3 = M3 (NaN)

M3A8_UN_M3 = M3 (NaN)

M3A9_UN_M3 = M3 (NaN)

M3B10_UN_M3 = M3 (NaN)

M3B3_UN_M3 = M3 (NaN)

M3B5_UN_M3 = M3 (NaN)

M3B6_UN_M3 = M3 (NaN)

M3B7_UN_M3 = M3 (NaN)

M3B8_UN_M3 = M3 (NaN)

M3B9_UN_M3 = M3 (NaN)

M3C1_UN_M3 = M3 (NaN)

M3C10_UN_M3 = M3 (NaN)

M3C2_UN_M3 = M3 (NaN)

M3C3_UN_M3 = M3 (NaN)

M3C4_UN_M3 = M3 (NaN)

M3C5_UN_M3 = M3 (NaN)

M3C7_UN_M3 = M3 (NaN)

M3C8_UN_M3 = M3 (NaN)

M3C9_UN_M3 = M3 (NaN)

M3D3_UN_M3 = M3 (NaN)

M3D4_UN_M3 = M3 (NaN)

M3D5_UN_M3 = M3 (NaN)

M3D6_UN_M3 = M3 (NaN)

M3D7_UN_M3 = M3 (NaN)

M3D8_UN_M3 = M3 (NaN)

M3D9_UN_M3 = M3 (NaN)

M3G10_UN_M3 = M3 (NaN)

HI1_UN_GRANA = GRANA (NaN)

HQ_UN_WDH = WDH (NaN)

HR_UN_WDH = WDH (NaN)

HS_UN_WDH = WDH (NaN)

HV_UN_SMLM = SMLM (NaN)

HJ2_UN_GRANA = GRANA (NaN)

HJ3_UN_GRANA = GRANA (NaN)

HJ4_UN_GRANA = GRANA (NaN)

HJ5_UN_GRANA = GRANA (NaN)

HJ6_UN_GRANA = GRANA (NaN)

HJ7_UN_GRANA = GRANA (NaN)

HJ8_UN_GRANA = GRANA (NaN)

HJ9_UN_GRANA = GRANA (NaN)

HJ10_UN_GRANA = GRANA (NaN)

HJ11_UN_GRANA = GRANA (NaN)

HJ12_UN_GRANA = GRANA (NaN)

HI2_UN_GRANA = GRANA (NaN)

HI3_UN_GRANA = GRANA (NaN)

HI4_UN_GRANA = GRANA (NaN)

HI5_UN_GRANA = GRANA (NaN)

HI6_UN_GRANA = GRANA (NaN)

HD1_UN_GRANA = GRANA (NaN)

HD2_UN_GRANA = GRANA (NaN)

HD3_UN_GRANA = GRANA (NaN)

HD4_UN_GRANA = GRANA (NaN)

HD1_UN_CADEQUES = CADEQUES (NaN)

HD2_UN_CADEQUES = CADEQUES (NaN)

HD3_UN_CADEQUES = CADEQUES (NaN)

HD4_UN_CADEQUES = CADEQUES (NaN)

HD5_UN_CADEQUES = CADEQUES (NaN)

HD6_UN_CADEQUES = CADEQUES (NaN)

HD7_UN_CADEQUES = CADEQUES (NaN)

HD8_UN_CADEQUES = CADEQUES (NaN)

HD9_UN_CADEQUES = CADEQUES (NaN)

HD10_UN_CADEQUES = CADEQUES (NaN)

HD11_UN_CADEQUES = CADEQUES (NaN)

HD12_UN_CADEQUES = CADEQUES (NaN)

HD13_UN_CADEQUES = CADEQUES (NaN)

HD14_UN_CADEQUES = CADEQUES (NaN)

HD15_UN_CADEQUES = CADEQUES (NaN)

HD16_UN_CADEQUES = CADEQUES (NaN)

HD17_UN_CADEQUES = CADEQUES (NaN)

HD18_UN_CADEQUES = CADEQUES (NaN)

HD19_UN_CADEQUES = CADEQUES (NaN)

HD20_UN_CADEQUES = CADEQUES (NaN)

HD21_UN_CADEQUES = CADEQUES (NaN)

HD22_UN_CADEQUES = CADEQUES (NaN)

HD23_UN_CADEQUES = CADEQUES (NaN)

CI73_UN_CI = CI (NaN)

1037 taxa

1 sites

1 patterns

TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore

======================================================

Please cite the following when publishing this model:

Remco Bouckaert, Joseph Heled, Denise Kuehnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc Suchard, Andrew Rambaut, Alexei J Drummond BEAST 2: A software platform for Bayesian evolutionary analysis. PLOS Computational Biology 10(4): e1003537, 2014

Hasegawa, M., Kishino, H and Yano, T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174.

======================================================

Start likelihood: -Infinity after 11 initialisation attempts

P(posterior) = -Infinity (was NaN)

P(prior) = -Infinity (was NaN)

P(CoalescentConstant.t:converted_TCS) = -2246.2855663595647 (was NaN)

P(ClockPrior.c:converted_TCS) = 0.0 (was NaN)

P(GammaShapePrior.s:converted_TCS) = -1.0 (was NaN)

P(KappaPrior.s:converted_TCS) = -1.8653600339742873 (was NaN)

P(nonZeroRatePrior.s:locations) = -Infinity (was NaN)

P(PopSizePrior.t:converted_TCS) = 1.2039728043259361 (was NaN)

P(relativeGeoRatesPrior.s:locations) = -1890.9999999999998 (was NaN)

P(geoclockPrior.c:locations) = -6.915086640662835 (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.converted_TCS) = NaN (was NaN)

P(traitedtreeLikelihood.locations) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at apple.launcher.LaunchRunner.run(LaunchRunner.java:116)

at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:51)

at apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)

[Remco Bouckaert]

Hi Catherine,

It looks like the nonZeroRatePrior.s:locations is causing problems — see
https://groups.google.com/forum/#!topic/beast-users/5LMllPcC26E

Cheers,

Remco

[shiva prakash]

Hi
Ramco

I am having hard time doing analysis in BEAST using starting tree. I always get this error. I went through the all the solutions posted in online discussion but I am not able solve this problem. This is what the
error I get. It will be great help, if you can help me to solve this problem. I am also attaching my xml file.


Thanks
Shiva

Random number seed: 1432152726634

File: Swamp2.xml seed: 1432152726634 threads: 1
Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
Start likelihood: -Infinity after 10 initialisation attempts

P(posterior) = -Infinity (was NaN)
    P(prior) = -Infinity (was NaN)

        P(YuleModel.t:tree) = -738146.9039392524 (was NaN)
        P(YuleBirthRatePrior.t:tree) = 0.0 (was NaN)
        P(GammaShapePrior.s:matk) = -1.638 (was NaN)
        P(GammaShapePrior.s:psba) = -2.637 (was NaN)
        P(GammaShapePrior.s:rbcl) = -0.30600000000000005 (was NaN)
        P(KappaPrior.s:rbcl) = -2.3967679465149976 (was NaN)
        P(PropInvariantPrior.s:matk) = 0.0 (was NaN)
        P(RateACPrior.s:matk) = -3.4493015967062974 (was NaN)
        P(RateACPrior.s:psba) = -3.4947495828573865 (was NaN)
        P(RateAGPrior.s:matk) = -4.111990107472738 (was NaN)
        P(RateAGPrior.s:psba) = -3.7564986995686165 (was NaN)
        P(RateATPrior.s:matk) = -3.0669992277009404 (was NaN)
        P(RateATPrior.s:psba) = -3.184008455701433 (was NaN)
        P(RateCGPrior.s:matk) = -3.297967740131271 (was NaN)
        P(RateCGPrior.s:psba) = -3.4947495828573865 (was NaN)
        P(RateCTPrior.s:matk) = -4.111990107472738 (was NaN)
        P(RateCTPrior.s:psba) = -4.005980141474587 (was NaN)
        P(RateGTPrior.s:matk) = -3.184008455701433 (was NaN)
        P(RateGTPrior.s:psba) = -3.184008455701433 (was NaN)
        P(MeanRatePrior.c:clock) = -1.4620820845188824 (was NaN)
        P(ucldStdevPrior.c:clock) = -2.3297588463941135 (was NaN)
        P(Arecales) = -Infinity (was NaN)
        P(Cornales) = NaN (was NaN)
        P(Ericales) = NaN (was NaN)
        P(Fabales) = NaN (was NaN)
        P(Lamiales) = NaN (was NaN)
        P(Laurales) = NaN (was NaN)
        P(Magnolids) = NaN (was NaN)
        P(Malphigiales) = NaN (was NaN)
        P(Malvales) = NaN (was NaN)
        P(Myrtales) = NaN (was NaN)
        P(Pandanales) = NaN (was NaN)
        P(Sapindales) = NaN (was NaN)
        P(PropInvariantPrior.s:psba) = 0.0 (was NaN)
        P(PropInvariantPrior.s:rbcl) = 0.0 (was NaN)

    P(likelihood) = NaN (was NaN)

        P(treeLikelihood.rbcl) = NaN (was NaN)
        P(treeLikelihood.matk) = NaN (was NaN)
        P(treeLikelihood.psba) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.
    at beast.core.MCMC.run(Unknown Source)
    at beast.app.BeastMCMC.run(Unknown Source)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)

    at beast.app.beastapp.BeastLauncher.main(Unknown Source)

[Remco Bouckaert]

The starting tree is not compatible with the first calibration, since the taxa(Caryota_urens, Pinanga_dicksonii) are not monophyletic in the starting tree while the calibration requires them to be monophyletic.

The second calibration is not compatible with the starting tree because it requires the clade to be of height at least 86, while the tree is lower than that.

To fix this, ensure that the starting tree is compatible with all calibrations.

Cheers,

Remco

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<Swamp2.xml>

[shiva prakash]

Hi Ramco

I am still having the same problem and getting the same error. I donot know what is the real problem, I tried all the option still it is not working. I am breaking my head to find out the problem. It is been two weeks, still I am not able to find out the problem. I really need your help. I am here by attaching the new xml file.

 File: Swafinal.xml seed: 1432782989615 threads: 1

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
Start likelihood: -Infinity after 10 initialisation attempts
P(posterior) = -Infinity (was NaN)
    P(prior) = -Infinity (was NaN)

        P(YuleModel.t:swamptree) = -1072770.4915427645 (was NaN)
        P(YuleBirthRatePrior.t:swamptree) = -Infinity (was NaN)

        P(GammaShapePrior.s:matk) = -1.638 (was NaN)
        P(GammaShapePrior.s:psba) = -2.637 (was NaN)
        P(GammaShapePrior.s:rbcl) = -0.30600000000000005 (was NaN)
        P(KappaPrior.s:rbcl) = -2.3967679465149976 (was NaN)
        P(PropInvariantPrior.s:matk) = 0.0 (was NaN)

        P(PropInvariantPrior.s:psba) = 0.0 (was NaN)
        P(PropInvariantPrior.s:rbcl) = 0.0 (was NaN)

        P(RateACPrior.s:matk) = -3.4493015967062974 (was NaN)
        P(RateACPrior.s:psba) = -3.4947495828573865 (was NaN)
        P(RateAGPrior.s:matk) = -4.111990107472738 (was NaN)
        P(RateAGPrior.s:psba) = -3.7564986995686165 (was NaN)

        P(RateATPrior.s:matk) = -1.606076332449436 (was NaN)

        P(RateATPrior.s:psba) = -3.184008455701433 (was NaN)
        P(RateCGPrior.s:matk) = -3.297967740131271 (was NaN)
        P(RateCGPrior.s:psba) = -3.4947495828573865 (was NaN)
        P(RateCTPrior.s:matk) = -4.111990107472738 (was NaN)
        P(RateCTPrior.s:psba) = -4.005980141474587 (was NaN)
        P(RateGTPrior.s:matk) = -3.184008455701433 (was NaN)
        P(RateGTPrior.s:psba) = -3.184008455701433 (was NaN)

        P(MeanRatePrior.c:clock) = 0.0 (was NaN)
        P(ucldStdevPrior.c:clock) = 0.819364145120802 (was NaN)

        P(Cornales) = NaN (was NaN)

        P(Malphigiales) = NaN (was NaN)
        P(Malvales) = NaN (was NaN)

        P(Sapindales) = NaN (was NaN)

    P(likelihood) = NaN (was NaN)
        P(treeLikelihood.rbcl) = NaN (was NaN)
        P(treeLikelihood.matk) = NaN (was NaN)
        P(treeLikelihood.psba) = NaN (was NaN)
java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.
    at beast.core.MCMC.run(Unknown Source)
    at beast.app.BeastMCMC.run(Unknown Source)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
    at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Thanks
Shiva

[pratap parida]

Hi,
Did you install beagle library.check whether it is installed peoperly. I am having the same problem. Just to ensure whether you are using windows or Linux?

Regards
Pratap

[shiva prakash]

Hi Pratap

I am using windows 7 and using BEAST 2. I have not installed beagle library.

Shiva

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[shiva prakash]

Hi Ramco

I had a lot of trouble using BEAST 2 and i thought I will use BEAST 1.8.2. But I am having trouble. It is giving the folowing error. I checked everything. Plz help I really need your help solving this. I am here by attaching my XMl file.

This is the error it gives. But the tree is closed with ")".

Parsing XML file: SwampNameedited2.xml

  File encoding: Cp1252

Looking for plugins in C:\Users\Shiva\Desktop\plugins

dr.xml.XMLParseException: Error parsing '<newick>' element with id, 'null':

error parsing tree in newick element - Missing closing ')' in tree

at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.parse(Unknown Source)

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

May 29, 2015 8:21:43 PM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed BEAST file, SwampNameedited2.xml:

Error parsing '<newick>' element with id, 'null':

error parsing tree in newick element - Missing closing ')' in tree

java.lang.RuntimeException: Terminate

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

Read alignment: alignment1

  Sequences = 210

      Sites = 496

   Datatype = nucleotide

Read alignment: alignment2

  Sequences = 210

      Sites = 846

   Datatype = nucleotide

Read alignment: alignment3

  Sequences = 210

      Sites = 395

   Datatype = nucleotide

Site patterns 'rbcl.patterns' created from positions 1-496 of alignment 'alignment1'

  unique pattern count = 289

Site patterns 'matk.patterns' created from positions 1-846 of alignment 'alignment2'

  unique pattern count = 742

Site patterns 'psba.patterns' created from positions 1-395 of alignment 'alignment3'

  unique pattern count = 375

Using Yule prior on tree

BEAST has terminated with an error. Please select QUIT from the menu.

Thanks

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[Nick Matzke]

Hi,

I haven't tried to run your file, but when I looked at the XML in a plain-text editor, I saw that there are several blank lines inserted inside the Newick string in your XML.  When I take these out, the resulting Newick loads in R at least:

See Slide #3 of this presentation for good advice on plain-text editors:

https://github.com/jeetsukumaran/2015-SSB-AnnArbor-Biogeography/blob/master/slides/biogeography-lab-biogeobears1.pdf

R code:

===============

library(ape)

trstr = "((((Gymnacranthera_canarica:58.116789,(Knema_attenuata:28.987257999999997,(Myristica_beddomei:14.509537999999992,(Myristica_malabarica:7.228056999999993,(Myristica_dactyloides:3.6222920000000016,Myristica_fatua:3.6222920000000016):3.605765000000005):7.281480999999999):14.477720000000005):29.129531):57.89892400000001,(((Neolitsea_zeylanica:54.03397700000001,((Actinodaphne_angustifolia:54.03397700000001,(Persea_macrantha:26.988409000000004,(Actinodaphne_hookeri:13.490921,((Cinnamomum_heyneanum:6.742157000000006,Cinnamomum_malabathrum:6.742157000000006):0.0,Cinnamomum_sulphuratum:6.742157000000006):6.748762999999997):13.497488000000004):27.045569):0.0,(Litsea_mysorensis:54.03397700000001,(Litsea_laevigata:26.994293,(Litsea_travancorica:13.494606000000005,(Actinodaphne_malabarica:6.747834999999995,(Litsea_floribunda:3.362922999999995,Litsea_stocksii:3.362922999999995):3.3849129999999974):6.746770999999995):13.499686999999994):27.03968400000001):0.0):0.0):53.96602299999999,(Cryptocarya_wightiana:53.989958,(Beilschmiedia_dalzellii:26.968812,Beilschmiedia_wightii:26.968812):27.021146):54.010042):3.804866000000004,(((Pandanus_tectorius:36.06013300000001,Pandanus_furcatus:36.06013300000001):35.575823,(Pinanga_dicksonii:35.898815,(Arenga_wightii:17.926470999999992,Caryota_urens:17.926470999999992):17.972344000000007):35.73714100000001):35.535602999999995,((Dillenia_pentagyna:98.895685,((((((((Melia_dubia:27.315267000000006,((((Reinwardtiodendron_anaimalaiense:9.192097000000004,(Aglaia_elaeagnoidea:4.583438000000001,(Aglaia_annamalayana:2.292856999999998,Aglaia_barberi:2.292856999999998):2.290581000000003):4.608659000000003):9.102193,Lansium_anamallayanum:18.294290000000004):0.0,(((Aglaia_lawii:9.173806999999996,Dysoxylum_binectariferum:9.173806999999996):9.120482999999993,Aglaia_roxburghiana:18.294290000000004):0.0,Dysoxylum_malabaricum:18.294290000000004):0.0):0.0,(Trichilia_connaroides:9.136718000000002,Walsura_trifolia:9.136718000000002):9.157572000000002):9.020977000000002):9.335825,(Toona_ciliata:17.872833999999997,Swietenia_macrophylla:17.872833999999997):18.778256999999996):9.098707000000005,(Vepris_bilocularis:22.903469,((Clausena_dentata:11.420052999999996,Atalantia_racemosa:11.420052999999996):0.0,Clausena_indica:11.420052999999996):11.483416000000005):22.846329999999995):8.769654000000003,(Sapindus_trifoliatus:27.844640999999996,Dimocarpus_longan:27.844640999999996):26.674812000000003):9.512157000000002,(Canarium_strictum:50.0,(Mangifera_indica:24.824596,((Holigarna_nigra:8.336002000000008,(Holigarna_arnottiana:4.170561000000006,(Holigarna_ferruginea:2.089110000000005,Holigarna_grahamii:2.089110000000005):2.0814510000000013):4.165441000000001):8.328205999999994,((Nothopegia_beddomei:8.284703000000007,(Nothopegia_racemosa:4.1502729999999985,Semecarpus_auriculata:4.1502729999999985):4.134429999999995):0.0,Semecarpus_kathalekanensis:8.284703000000007):8.379503999999997):8.160388999999995):25.175404):14.031610000000015):14.053305999999992,((Sterculia_guttata:32.43445700000001,(Leptonychia_moacurroides:16.015607000000003,Pterygota_alata:16.015607000000003):16.418849999999992):32.565543000000005,(Gnidia_glauca:32.18652300000001,((Bombax_ceiba:10.769557000000006,Helictres_isora:10.769557000000006):10.378367999999995,(Vateria_indica:11.144075,(Dipterocarpus_indicus:5.288846000000007,(Hopea_canarensis:2.7514429999999948,(Hopea_parviflora:1.3532919999999962,(Hopea_utilis:0.6633829999999961,Hopea_ponga:0.6633829999999961):0.6899090000000001):1.3981509999999986):2.537402):5.855228999999994):10.00385):11.038597999999993):32.813477000000006):13.084915999999993):13.54067599999999,(((Lagerstroemia_microcarpa:29.700266999999997,(Lagerstroemia_lanceolata:14.607854000000003,Lagerstroemia_speciosa:14.607854000000003):15.092412999999993):28.595397000000006,((Memecylon_amplexicaule:20.085182000000003,(Memecylon_malabaricum:9.786309000000003,(Memecylon_wightii:4.892497000000006,(Memecylon_randerianum:2.428642999999994,Memecylon_umbellatum:2.428642999999994):2.4638539999999978):4.893811999999997):10.298873):18.367131999999998,(Eugenia_macrocephala:19.574187999999992,(((Syzygium_canarana:6.494781000000003,Syzygium_zeylanicum:6.494781000000003):0.0,Syzygium_gardneri:6.494781000000003):6.561087000000001,((Syzygium_laetum:4.334046999999998,Syzygium_travancoricum:4.334046999999998):4.353104999999999,(((Syzygium_caryophyllatum:4.339357000000007,Syzygium_mundagam:4.339357000000007):0.0,(Syzygium_hemisphericum:4.339357000000007,Syzygium_lanceolatum:4.339357000000007):0.0):0.0,(Syzygium_cumini:4.339357000000007,Syzygium_heyneanum:4.339357000000007):0.0):4.347796000000002):4.368716000000006):6.518320000000003):18.87812600000001):19.84335):29.704335,(Terminalia_elliptica:44.240628,(Terminalia_bellirica:21.96889300000001,Terminalia_paniculata:21.96889300000001):22.271734999999993):43.759372):3.6255919999999975):3.973708000000002,(((Tetrameles_nudiflora:23.497625999999997,(Celtis_philippensis:11.769501000000005,(Dendrocnide_sinuata:5.588560999999999,((Artocarpus_heterophyllus:2.010552000000004,(Artocarpus_hirsutus:0.9952130000000068,Artocarpus_integrifolia:0.9952130000000068):1.0153389999999973):1.9429899999999947,(Ficus_bedomi:1.8238640000000004,((Ficus_amplissima:1.0018309999999957,(Ficus_nervosa:1.0018309999999957,Ficus_hispida:1.0018309999999957):0.0):0.0,(Ficus_callosa:0.4865559999999931,Ficus_tsjahela:0.4865559999999931):0.5152750000000026):0.8220330000000047):2.1296779999999984):1.6350189999999998):6.1809399999999926):11.728125000000006):24.233449000000007,(Xanthophyllum_arnottianum:23.634071000000006,((Erythrina_variegata:7.295018999999996,(Humboldtia_brunonis:4.026255000000006,Kingiodendron_pinnatum:4.026255000000006):3.268763000000007):8.530308000000005,(Bauhinia_purpurea:7.709074000000001,(Archidendron_monadelphum:3.1904729999999972,Dalbergia_latifolia:3.1904729999999972):4.518601000000004):8.116253):7.808744000000004):24.097004999999996):23.893818999999993,((Lophopetalum_wightianum:24.141082999999995,(Euonymus_angulatus:11.985185999999999,Euonymus_indicus:11.985185999999999):12.155897999999993):23.316699,((Elaeocarpus_glandulosus:16.217062999999996,(Elaeocarpus_serratus:7.967175999999995,Elaeocarpus_tuberculatus:7.967175999999995):8.249887000000001):15.197449000000006,(((Carallia_brachiata:7.4626090000000005,Erythroxylum_lanceolatum:7.4626090000000005):8.222890000000007,((((Garcinia_talbotii:5.452476000000004,Garcinia_gummigutta:5.452476000000004):0.0,Garcinia_xanthochymus:5.452476000000004):0.0,Garcinia_morella:5.452476000000004):5.076291999999995,(Poeciloneuron_indicum:5.293847999999997,(Mesua_ferrea:2.6495409999999993,(Calophyllum_apetalum:1.3209080000000029,Calophyllum_polyanthum:1.3209080000000029):1.3286329999999964):2.6443069999999977):5.2349200000000025):5.156729999999996):8.284082999999995,(((Hydnocarpus_pentandra:7.639972999999998,(Rinorea_bengalensis:3.521951999999999,(Homalium_zeylanicum:2.0749560000000002,Scolopia_crenata:2.0749560000000002):1.4469959999999986):4.118020999999999):8.270084999999995,(Flacourtia_montana:7.790572999999995,(Casearia_ovata:4.038927000000001,(Casearia_championii:1.9518520000000024,(Casearia_glomerata:1.0076090000000022,Casearia_rubescens:1.0076090000000022):0.9442430000000002):2.0870749999999987):3.751645999999994):8.119484999999997):8.059523999999996,((((Epiprinus_mallotiformis:6.120356000000001,(Croton_malabaricus:2.952729000000005,Fahrenheitia_zeylanica:2.952729000000005):3.1676279999999934):5.778745999999998,(Dimorphocalyx_beddomei:5.870921999999993,((Agrostistachys_indica:1.984967999999995,Agrostistachys_meeboldii:1.984967999999995):2.0013620000000003,(Mallotus_stenanthus:1.7635669999999948,(Macaranga_peltata:1.0580520000000035,(Trewia_nudiflora:0.46059200000000544,(Mallotus_philippensis:0.018304999999998017,Mallotus_tetracoccus:0.018304999999998017):0.4422869999999932):0.5974599999999981):0.7055150000000054):2.222763999999998):1.8845910000000003):6.028180000000006):5.699613999999997,(Drypetes_elata:9.081356,Drypetes_wightii:9.081356):8.517359999999996):6.370864999999995,(Antidesma_menasu:11.476854000000003,((Bischofia_javanica:3.800229999999999,(Baccaurea_courtalensis:2.109970000000004,(Aporosa_acuminata:0.9683349999999962,(Aporosa_lindleyana:0.4977130000000045,(Aporosa_bourdillonii:0.23420099999999877,Aporosa_cardiosperma:0.23420099999999877):0.26351200000000574):0.47062300000000334):1.1416339999999963):1.690259999999995):4.153837999999993,(Bridelia_retusa:3.4702350000000024,(Phyllanthus_emblica:2.294521000000003,((Glochidion_zeylanicum:1.0170109999999966,Glochidion_malabaricum:1.0170109999999966):0.0,Glochidion_ellipticum:1.0170109999999966):1.2775100000000066):1.1757149999999967):4.483833000000004):3.5227859999999964):12.492728):0.0):0.0):7.444929999999999):16.043271000000004):24.167112000000003):23.974407):3.2963840000000033):4.496957000000009,(Strombosia_ceylanica:98.580747,(((Careya_arborea:44.969106,((Symplocos_macrophylla:15.088999999999999,(Symplocos_cochinchinensis:7.493733000000006,Symplocos_racemosa:7.493733000000006):7.595267000000007):14.800442000000004,((((Diospyros_crumenata:4.9778479999999945,(Diospyros_sylvatica:2.472336999999996,(Diospyros_pruriens:1.2404920000000033,(Diospyros_paniculata:0.6216210000000046,(Diospyros_foliosa:0.29695999999999856,Diospyros_saldanha:0.29695999999999856):0.3246610000000061):0.6188709999999986):1.2318460000000044):2.5055109999999985):5.097622999999999,(Diospyros_buxifolia:4.9935059999999964,Diospyros_angustifolia:4.9935059999999964):5.081964999999997):0.0,Diospyros_candolleana:10.075470999999993):9.678683000000007,((Chrysophyllum_lanceolatum:6.673662000000007,Chrysophyllum_roxburghii:6.673662000000007):6.794850999999994,(Madhuca_neriifolia:6.658140000000003,(Palaquium_elliipticum:3.325981999999996,(Madhuca_longifolia:1.6337950000000063,Mimusops_elengi:1.6337950000000063):1.692187000000004):3.332158000000007):6.8103729999999985):6.285641999999996):10.135288000000003):15.079662999999996):45.030894,((Schleichera_oleosa:30.110442000000006,(Schefflera_capitata:14.998571999999996,Schefflera_venulosa:14.998571999999996):15.111871000000008):29.671620999999995,((Apodytes_dimidiata:19.479301000000007,Nothapodytes_nimmoniana:19.479301000000007):20.476754999999997,((Stereospermum_colais:12.964909000000006,(Chionanthus_malabaricus:6.7113549999999975,Olea_dioica:6.7113549999999975):6.253555000000006):13.557564999999997,(((Mitragyna_parvifolia:6.788769000000002,((Neonauclea_purpurea:3.2897899999999964,Neolamarckia_cadamba:3.2897899999999964):0.0,Mitragyna_tubulosa:3.2897899999999964):3.4989790000000056):6.456849000000005,(((Pavetta_indica:4.188496999999998,Gardenia_obtusa:4.188496999999998):0.0,Canthium_dicoccum:4.188496999999998):4.772354000000007,(Ixora_brachiata:4.356144999999998,(Meyna_laxiflora:2.189143999999999,(Canthium_angustifolium:1.1375730000000033,Catunaregam_dumetorum:1.1375730000000033):1.0515709999999956):2.167000999999999):4.604705999999993):4.284767000000002):6.625484,(Strychnos_nuxvomica:9.774282,(Alstonia_scholaris:4.847787999999994,(Anodendron_paniculatum:2.164438000000004,(Tabernaemontana_alternifolia:1.3154399999999953,Tabernaemontana_heyneana:1.3154399999999953):0.8489979999999946):2.683349000000007):4.926494000000005):10.096818999999996):6.651373000000007):13.433582000000001):19.826006999999997):30.217937):4.4120610000000084,(Alangium_salviifolium:86.0,Mastixia_arborea:86.0):8.412061000000008):4.168685999999994):4.811895000000007):3.7789169999999928):4.633307000000002):4.210846000000004):3.984286999999995,Polyalthia_fragrans:120.0):0.0,Meiogyne_pannosa:120.0);"

tr = read.tree(file="", text=trstr)

tr

===============

[shiva prakash]

Hi

Nick

Thank you very much. It is running now. But how to find those blank line and get rid of them. I open file in Notepad++ text editor but I was not able to find them. Plz let me know how to find these blank lines and delete them using Notepad++. You let me know is there any R code to do that.

Thank you.

Shiva.

[Nick Matzke]

If you turn on line-numbering in Notetab++, you should be able to see the difference between line breaks and no line breaks:

https://www.youtube.com/watch?v=s8TouX89NBo

[Beth B]

Hi Remco,

I'm trying to apply total evidence dating with a fossilised birth death model with 21 taxa, of which one of the taxa is a fossil. There are seven gene partitions and 1 morphology partition. Unfortunately, I can't get BEAST 2.3.1 to run as I'm having a similar problem with the "Start likelihood: NaN". Below is the log file. 

File: 151111_mt_s_EO_beast2.3.1_try2.xml seed: 1447267776970 threads: 8

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 8 unique site patterns.

  Using rescaling scheme : dynamic

java.lang.NullPointerException

at beast.evolution.likelihood.BeagleTreeLikelihood.setUpSubstModel(Unknown Source)

at beast.evolution.likelihood.BeagleTreeLikelihood.initialize(Unknown Source)

at beast.evolution.likelihood.BeagleTreeLikelihood.initAndValidate(Unknown Source)

at beast.core.BEASTInterface.initByName(Unknown Source)

at beast.evolution.likelihood.TreeLikelihood.initAndValidate(Unknown Source)

at beast.util.XMLParser.initPlugins(Unknown Source)

at beast.util.XMLParser.parse(Unknown Source)

at beast.util.XMLParser.parseFile(Unknown Source)

at beast.app.BeastMCMC.parseArgs(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 7 unique site patterns.

  Using r  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

escaling scheme : dynamic

java.lang.NullPointerException

at beast.evolution.likelihood.BeagleTreeLikelihood.setUpSubstModel(Unknown Source)

at beast.evolution.likelihood.BeagleTreeLikelihood.initialize(Unknown Source)

at beast.evolution.likelihood.BeagleTreeLikelihood.initAndValidate(Unknown Source)

at beast.core.BEASTInterface.initByName(Unknown Source)

at beast.evolution.likelihood.TreeLikelihood.initAndValidate(Unknown Source)

at beast.util.XMLParser.initPlugins(Unknown Source)

at beast.util.XMLParser.parse(Unknown Source)

at beast.util.XMLParser.parseFile(Unknown Source)

at beast.app.BeastMCMC.parseArgs(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 68 unique site patterns.

  Using rescaling scheme : dynamic

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 54 uni  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

que site patterns.

  Using rescaling scheme : dynamic

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 25 unique site patterns.

  Using rescaling scheme : dynamic

  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Using BEAGLE version: 2.1.2 resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 23 unique site patterns.

  Using rescaling scheme : dynamic

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 29 unique site patterns.

  Using rescaling scheme : dynamic

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 57 unique site patterns.

  Using rescaling scheme : dynamic

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 69 unique site patterns.

  Using rescaling scheme : dynamic

Start likelihood: NaN 

P(posterior) = NaN (was NaN)

P(prior) = NaN (was NaN)

P(FBD.t:151111_binary_eopoly_subs_BEAST2) = NaN (was NaN)

P(GammaShapePrior.s:nad5_intron_subs_EO) = -1.0 (was NaN)

P(GammaShapePrior.s:rbcL_12codon_subs_EO) = -1.0 (was NaN)

P(GammaShapePrior.s:trnLFspacer_subs_EO) = -1.0 (was NaN)

P(KappaPrior.s:nad5_exon1and2_rps4genemin9_c12_subs_EO) = -1.8653600339742873 (was NaN)

P(RateACPrior.s:nad5_exon1and2_rps4min9_c3_subs_EO) = -3.184008455701433 (was NaN)

P(RateACPrior.s:nad5_intron_subs_EO) = -3.184008455701433 (was NaN)

P(RateACPrior.s:rbcL_12codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateACPrior.s:rbcL_3codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateACPrior.s:rps4trnSspacer_subs_EO) = -3.184008455701433 (was NaN)

P(RateACPrior.s:trnLFspacer_subs_EO) = -3.184008455701433 (was NaN)

P(RateAGPrior.s:nad5_exon1and2_rps4min9_c3_subs_EO) = -3.1686658147294304 (was NaN)

P(RateAGPrior.s:nad5_intron_subs_EO) = -3.1686658147294304 (was NaN)

P(RateAGPrior.s:rbcL_12codon_subs_EO) = -3.1686658147294304 (was NaN)

P(RateAGPrior.s:rbcL_3codon_subs_EO) = -3.1686658147294304 (was NaN)

P(RateAGPrior.s:rps4trnSspacer_subs_EO) = -3.1686658147294304 (was NaN)

P(RateAGPrior.s:trnLFspacer_subs_EO) = -3.1686658147294304 (was NaN)

P(RateATPrior.s:nad5_exon1and2_rps4min9_c3_subs_EO) = -3.184008455701433 (was NaN)

P(RateATPrior.s:nad5_intron_subs_EO) = -3.184008455701433 (was NaN)

P(RateATPrior.s:rbcL_12codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateATPrior.s:rbcL_3codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateATPrior.s:rps4trnSspacer_subs_EO) = -3.184008455701433 (was NaN)

P(RateATPrior.s:trnLFspacer_subs_EO) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:nad5_exon1and2_rps4min9_c3_subs_EO) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:nad5_intron_subs_EO) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:rbcL_12codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:rbcL_3codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:rps4trnSspacer_subs_EO) = -3.184008455701433 (was NaN)

P(RateCGPrior.s:trnLFspacer_subs_EO) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:nad5_exon1and2_rps4min9_c3_subs_EO) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:nad5_intron_subs_EO) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:rbcL_12codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:rbcL_3codon_subs_EO) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:rps4trnSspacer_subs_EO) = -3.184008455701433 (was NaN)

P(RateGTPrior.s:trnLFspacer_subs_EO) = -3.184008455701433 (was NaN)

P(MeanRatePrior.c:151111_binary_eopoly_subs_BEAST23) = 0.0 (was NaN)

P(MeanRatePrior.c:nad5_exon1and2_rps4genemin9_c12_subs_EO) = 0.0 (was NaN)

P(MeanRatePrior.c:nad5_exon1and2_rps4min9_c3_subs_EO) = 0.0 (was NaN)

P(MeanRatePrior.c:nad5_intron_subs_EO) = 0.0 (was NaN)

P(MeanRatePrior.c:rbcL_12codon_subs_EO) = 0.0 (was NaN)

P(MeanRatePrior.c:rbcL_3codon_subs_EO) = 0.0 (was NaN)

P(MeanRatePrior.c:rps4trnSspacer_subs_EO) = 0.0 (was NaN)

P(MeanRatePrior.c:trnLFspacer_subs_EO) = 0.0 (was NaN)

P(ucldStdevPrior.c:151111_binary_eopoly_subs_BEAST23) = 0.819364145120802 (was NaN)

P(ucldStdevPrior.c:nad5_exon1and2_rps4genemin9_c12_subs_EO) = 0.819364145120802 (was NaN)

P(ucldStdevPrior.c:nad5_exon1and2_rps4min9_c3_subs_EO) = 0.819364145120802 (was NaN)

P(ucldStdevPrior.c:nad5_intron_subs_EO) = 0.819364145120802 (was NaN)

P(ucldStdevPrior.c:rbcL_12codon_subs_EO) = 0.819364145120802 (was NaN)

P(ucldStdevPrior.c:rbcL_3codon_subs_EO) = 0.819364145120802 (was NaN)

P(ucldStdevPrior.c:rps4trnSspacer_subs_EO) = 0.819364145120802 (was NaN)

P(ucldStdevPrior.c:trnLFspacer_subs_EO) = 0.819364145120802 (was NaN)

P(likelihood) = NaN (was NaN)

P(morphTreeLikelihood.151111_binary_eopoly_subs_BEAST22) = NaN (was NaN)

P(morphTreeLikelihood.151111_binary_eopoly_subs_BEAST23) = NaN (was NaN)

P(treeLikelihood.nad5_exon1and2_rps4genemin9_c12_subs_EO) = NaN (was NaN)

P(treeLikelihood.nad5_exon1and2_rps4min9_c3_subs_EO) = NaN (was NaN)

P(treeLikelihood.nad5_intron_subs_EO) = NaN (was NaN)

P(treeLikelihood.rbcL_3codon_subs_EO) = NaN (was NaN)

P(treeLikelihood.rbcL_12codon_subs_EO) = NaN (was NaN)

P(treeLikelihood.rps4trnSspacer_subs_EO) = NaN (was NaN)

P(treeLikelihood.trnLFspacer_subs_EO) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Also, I have one more general question: why is it that, as soon as I upload a morphology nex file (and whether that is my own or the one from the http://beast2.org/total-evidence-with-fbd-dating/ tutorial) Beauti immediately splits the file into two or more partitions? And when I click on the partitions they contain dots and different numbers than the one I provided. I was just curious what's happening, although since the same happens with the tutorial morphology nex file I don't think this is the cause of my problem.

Thanks so much for taking the time to help me - I've spend several hours trying to solve this and really don't know what I could change..

Best wishes,

Beth

On Monday, July 14, 2014 at 9:28:06 PM UTC+1, Norm wrote:

Hi, 

I've been having a hard time tracking down the errors when trying to run *BEAST.

The first mistake I had was that not every species was represented in every alignment. I rectified that in a quick and dirty way, by adding a single dummy sequence assigned to each species. Everything else is set according to the *BEAST tutorial. There is a fair amount of missing data in these alignments, since it was from a sequence-capture experiment. I'm just hoping that it's an error in the settings, and not a problem with trying to analyze this particular dataset. 

I will attach the xml. 

Thanks for any advice!

======================================================

Start likelihood: -Infinity after 11 initialisation attempts

P(posterior) = -Infinity (was NaN)

P(speciescoalescent) = -3.3262019264778784E11 (was NaN)

P(SpeciesTreePopSize.Species) = 690.8014759618696 (was NaN)

P(treePrior.t:AT1G01290dum_aln) = -9.642816448055316E10 (was NaN)

P(treePrior.t:AT1G12800dum_aln) = -1.2771911205960396E11 (was NaN)

P(treePrior.t:AT1G18190dum_aln) = -1.0847291679843216E11 (was NaN)

P(prior) = -Infinity (was NaN)

P(YuleModel.t:Species) = 211.30666951105965 (was NaN)

P(YuleBirthRatePrior.t:Species) = -5.362240542149371 (was NaN)

P(ClockPrior.c:AT1G01290dum_aln) = 0.0 (was NaN)

P(ClockPrior.c:AT1G18190dum_aln) = 0.0 (was NaN)

P(KappaPrior.s:AT1G01290dum_aln) = -1.8653600339742873 (was NaN)

P(KappaPrior.s:AT1G12800dum_aln) = -1.8653600339742873 (was NaN)

P(KappaPrior.s:AT1G18190dum_aln) = -1.8653600339742873 (was NaN)

P(popMean.prior) = 0.0 (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.AT1G12800dum_aln) = NaN (was NaN)

P(treeLikelihood.AT1G18190dum_aln) = NaN (was NaN)

P(treeLikelihood.AT1G01290dum_aln) = NaN (was NaN)

[Beth B]

Hi all,

I already managed to fix it - going through the tutorial and setting up the analysis from scratch again. I must have made a mistake somewhere..

[janex...@gmail.com]

Hi Remco an others here,

         I'm frustrated by the same issue, and tried the suggestions you gave but failed once more. 

         One of my four loci lack sequences of 4 taxa, thus I give ??? for the full length, the same error come out.

         Next I just deleted the locus lacking taxa, the error still there!          

======================================================

Start likelihood: NaN 

P(posterior) = NaN (was NaN)

P(speciescoalescent) = NaN (was NaN)

P(SpeciesTreePopSize.Species) = NaN (was NaN)

P(treePrior.t:Cytb_PaAe17spstre) = NaN (was NaN)

P(treePrior.t:aA_PaAe17_consA) = NaN (was NaN)

P(treePrior.t:bA_PaAe17_consA) = NaN (was NaN)

P(prior) = NaN (was NaN)

P(YuleModel.t:Species) = NaN (was NaN)

P(YuleBirthRatePrior.t:Species) = -5.362240542149371 (was NaN)

P(ClockPrior.c:Cytb_PaAe17spstre) = -1.4620820845188824 (was NaN)

P(ClockPrior.c:bA_PaAe17_consA) = -1.4620820845188824 (was NaN)

P(MutationRatePrior.s:Cytb_PaAe17spstre) = -1.4620820845188824 (was NaN)

P(MutationRatePrior.s:aA_PaAe17_consA) = -1.8862943611198906 (was NaN)

P(MutationRatePrior.s:bA_PaAe17_consA) = -1.8862943611198906 (was NaN)

P(popMean.prior) = 0.0 (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.aA_PaAe17_consA) = NaN (was NaN)

P(treeLikelihood.bA_PaAe17_consA) = NaN (was NaN)

P(treeLikelihood.Cytb_PaAe17spstre) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

              And I also tried v1.8.4, the different error reported as follow, I've no idea what it means and can't find the incorrectly construction of the sequence.

===============================================================

        SEVERE: Parsing error - poorly formed BEAST file, Tits_3loci_tree1e7.xml:

The '<sequence>' element with id, 'seq_Ae_bonvaloti6', is incorrectly constructed.

The following was expected:

Exactly one ELEMENT of type Taxon REQUIRED

java.lang.RuntimeException: Terminate

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

            I'm so appreciate if any of you would like to help me figure it out! Hope it won't cost a year......

            Happy new year and best wishes!!

Jane   

[Denis Marques]

Hi, Remco! I am having a problem when i try to run BEAST v.2.4.4 for Extended Bayesian Skyline Plot. I had try to change the Invariant to 0, in the F sequence, but not solved. This is the error that shows to me:

Start likelihood: Infinity after 10 initialisation attempts

P(posterior) = Infinity (was Infinity)

P(prior) = Infinity (was Infinity)

P(ExtendedBayesianSkyline.t:Fno_duplication_DNA_resumido_alinhado) = -230.48894385874684 (was -230.48894385874684)

P(ExtendedBayesianSkyline.t:Gno_duplication_DNA_resumido_alinhado) = -223.29720880707234 (was -223.29720880707234)

P(ExtendedBayesianSkyline.t:M22_no_duplication_edited_DNA_resumido) = -240.90684295593883 (was -240.90684295593883)

P(ClockPrior.c:M22_no_duplication_edited_DNA_resumido) = 0.0 (was 0.0)

P(GammaShapePrior.s:Gno_duplication_DNA_resumido_alinhado) = -1.4620820845188824 (was -1.4620820845188824)

P(indicatorsPrior.alltrees) = -0.69314718056 (was -0.69314718056)

P(kappa1Prior.s:M22_no_duplication_edited_DNA_resumido) = -1.8653600339742873 (was -1.8653600339742873)

P(kappa2Prior.s:M22_no_duplication_edited_DNA_resumido) = -1.8653600339742873 (was -1.8653600339742873)

P(popSizePrior.alltrees) = -667.0 (was -667.0)

P(populationMeanPrior.alltrees) = 0.0 (was 0.0)

P(PropInvariantPrior.s:Fno_duplication_DNA_resumido_alinhado) = 0.0 (was 0.0)

P(RateACPrior.s:Fno_duplication_DNA_resumido_alinhado) = 0.6304133994553054 (was 0.6304133994553054)

P(RateACPrior.s:Gno_duplication_DNA_resumido_alinhado) = 0.6304133994553054 (was 0.6304133994553054)

P(RateAGPrior.s:Fno_duplication_DNA_resumido_alinhado) = -1.0272546471991955 (was -1.0272546471991955)

P(RateAGPrior.s:Gno_duplication_DNA_resumido_alinhado) = -0.2752201548531391 (was -0.2752201548531391)

P(RateATPrior.s:Fno_duplication_DNA_resumido_alinhado) = 1.2899032209872534 (was 1.2899032209872534)

P(RateATPrior.s:Gno_duplication_DNA_resumido_alinhado) = 0.6304133994553054 (was 0.6304133994553054)

P(RateCGPrior.s:Fno_duplication_DNA_resumido_alinhado) = Infinity (was Infinity)

P(RateCGPrior.s:Gno_duplication_DNA_resumido_alinhado) = Infinity (was Infinity)

P(RateCTPrior.s:Fno_duplication_DNA_resumido_alinhado) = -1.9571851765278938 (was -1.9571851765278938)

P(RateCTPrior.s:Gno_duplication_DNA_resumido_alinhado) = -0.835Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

6174865101518 (was -0.8356174865101518)

P(RateGTPrior.s:Fno_duplication_DNA_resumido_alinhado) = 0.6304133994553054 (was 0.6304133994553054)

P(RateGTPrior.s:Gno_duplication_DNA_resumido_alinhado) = 0.6304133994553054 (was 0.6304133994553054)

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.Fno_duplication_DNA_resumido_alinhado) = NaN (was NaN)  **

P(treeLikelihood.Gno_duplication_DNA_resumido_alinhado) = NaN (was NaN)  **

P(treeLikelihood.M22_no_duplication_edited_DNA_resumido) = NaN (was NaN)  **

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

BEAST has terminated with an error. Please select QUIT from the menu.

Could you help me, please? Attached is my xml file.

[Remco Bouckaert]

Hi Denis,

The reason the analysis does not start is that there is a gamma prior on both of the CG rates, but these rates are initialised to be zero, and the gamma distribution has zero support for that value. So, the output says:

P(RateCGPrior.s:Fno_duplication_DNA_resumido_alinhado) = Infinity (was Infinity)
P(RateCGPrior.s:Gno_duplication_DNA_resumido_alinhado) = Infinity (was Infinity)

To prevent this from happening, you can change the start value of the CG rates to something small, or you can change the prior to some other distribution, one which has support for the value zero.

Cheers,

Remco

[Keir Wefferling]

Hi Remco et al., 

Sorry to say I'm getting the same error message with 2_2_17Ranuncs1.xml. I got a previous version of this dataset to run (Ranunculales copy2.xm) with several big differences: in the latter there are fewer partitions, site models are specified (as opposed to utilizing model averaging with bModelTest), and using a strict clock rather than relaxed lognormal. Any help would be greatly appreciated!

                        BEAST v2.4.4, 2002-2016

             Bayesian Evolutionary Analysis Sampling Trees

                       Designed and developed by

 Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

                                    

                 ...

Random number seed: 1486067559173

Alignment(mcRan1_4loci)

  98 taxa

  5413 sites

  3001 patterns

Filter 1-1534\3

98 taxa

512 sites

434 patterns

  UCRelaxedClockModel: using 194 rate categories to approximate rate distribution across branches.

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 2-1535\3

98 taxa

512 sites

383 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 3-1536\3

98 taxa

512 sites

471 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 1537-2992\3

98 taxa

486 sites

190 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 1538-2993\3

98 taxa

486 sites

159 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 1539-2994\3

98 taxa

486 sites

414 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 2995-4381\3

98 taxa

463 sites

226 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 2996-4382\3

98 taxa

463 sites

202 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 2997-4383\3

98 taxa

463 sites

394 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

Filter 4384-5413

98 taxa

1030 sites

390 patterns

  Using BEAGLE version: 1.x resource 0: CPU

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU

===============================================================================

Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA,

  Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian

  evolutionary analysis. PLoS Computational Biology 10(4): e1003537

Heled J, Drummond AJ (2012) Calibrated Tree Priors for Relaxed Phylogenetics

  and Divergence Time Estimation. Systematic Biology 61(1):138-149.

Remco Bouckaert. bModelTest: Bayesian site model selection for nucleotide data. BioRxiv 2015/06/11/020792

Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and

  Dating with Confidence. PLoS Biol 4(5): e88

===============================================================================

Start likelihood: NaN 

P(posterior) = NaN (was NaN)  **

P(prior) = NaN (was NaN)  **

P(CalibratedYuleModel.t:Ranuncs1tree) = NaN (was NaN)  **

P(BMT_PropInvariablePrior.s:26S) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:atpB_pos1) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:atpB_pos2) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:atpB_pos3) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:matK_pos1) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:matK_pos2) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:matK_pos3) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:rbcL_pos1) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:rbcL_pos2) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_PropInvariablePrior.s:rbcL_pos3) = 1.0702128141464131 (was 1.0702128141464131)

P(BMT_RatesPrior.s:26S) = NaN (was NaN)  **

P(BMT_RatesPrior.s:atpB_pos1) = NaN (was NaN)  **

P(BMT_RatesPrior.s:atpB_pos2) = NaN (was NaN)  **

P(BMT_RatesPrior.s:atpB_pos3) = NaN (was NaN)  **

P(BMT_RatesPrior.s:matK_pos1) = NaN (was NaN)  **

P(BMT_RatesPrior.s:matK_pos2) = NaN (was NaN)  **

P(BMT_RatesPrior.s:matK_pos3) = NaN (was NaN)  **

P(BMT_RatesPrior.s:rbcL_pos1) = NaN (was NaN)  **

P(BMT_RatesPrior.s:rbcL_pos2) = NaN (was NaN)  **

P(BMT_RatesPrior.s:rbcL_pos3) = NaN (was NaN)  **

P(BMT_freqsPrior.s:26S) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:atpB_pos1) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:atpB_pos2) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:atpB_pos3) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:matK_pos1) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:matK_pos2) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:matK_pos3) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:rbcL_pos1) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:rbcL_pos2) = 1.791759469228056 (was 1.791759469228056)

P(BMT_freqsPrior.s:rbcL_pos3) = 1.791759469228056 (was 1.791759469228056)

P(BMT_GammaShapePrior.s:26S) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:atpB_pos1) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:atpB_pos2) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:atpB_pos3) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:matK_pos1) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:matK_pos2) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:matK_pos3) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:rbcL_pos1) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:rbcL_pos2) = -1.0 (was -1.0)

P(BMT_GammaShapePrior.s:rbcL_pos3) = -1.0 (was -1.0)

P(CalibratedYuleBirthRatePrior.t:Ranuncs1tree) = -6.915086640662835 (was -6.915086640662835)

P(MeanRatePrior.c:Clock Model) = 0.0 (was 0.0)

P(ucldStdevPrior.c:Clock Model) = 0.819364145120802 (was 0.819364145120802)

P(Cocculus.prior) = NaN (was NaN)  **

P(EudicotFatal exception: Could not find a proper state to initialise. Perhaps try another seed.

s.prior) = NaN (was NaN)  **

P(Hypserpa.prior) = NaN (was NaN)  **

P(Kajanthus.prior) = NaN (was NaN)  **

P(Lardizabalaceae.prior) = NaN (was NaN)  **

P(Mahonia.prior) = NaN (was NaN)  **

P(Proteales.prior) = NaN (was NaN)  **

P(SACC.prior) = NaN (was NaN)  **

P(Tinospora.prior) = NaN (was NaN)  **

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.matK_pos1) = NaN (was NaN)  **

P(treeLikelihood.matK_pos2) = NaN (was NaN)  **

P(treeLikelihood.matK_pos3) = NaN (was NaN)  **

P(treeLikelihood.atpB_pos1) = NaN (was NaN)  **

P(treeLikelihood.atpB_pos2) = NaN (was NaN)  **

P(treeLikelihood.atpB_pos3) = NaN (was NaN)  **

P(treeLikelihood.rbcL_pos1) = NaN (was NaN)  **

P(treeLikelihood.rbcL_pos2) = NaN (was NaN)  **

P(treeLikelihood.rbcL_pos3) = NaN (was NaN)  **

P(treeLikelihood.26S) = NaN (was NaN)  **

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

BEAST has terminated with an error. Please select QUIT from the menu.

[Remco Bouckaert]

Hi Kier,

It looks like the problem is caused by the CalibratedYuleModel not behaving quite as expected, perhaps due to numerical issues. I am investigating what is going wrong, but if you want to get the analysis going, replacing the CalibratedYuleModel with the YuleModel will do so. I’ll let you know when I know more about the source of the problem and whether there is a more elegant fix for this.

Cheers,

Remco

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<2_2_17Ranuncs1.xml><Ranunculales copy2.xml>

[Keir Wefferling]

Thank you, Remco!

An update: I've had much better luck with the Birth-Death or Yule tree prior (as you suggest).

All the best, Keir

[Alice Gerlach]

Hi beast users!

I try to run analyses on template stacey Beast 2 v.2.4.4

with the same prior that worked in the last analyses I done with dataset 69 specimens for 3 markers and without missing data.

Now the dataset presents 174 taxa (without missing data) and the error "could not find a proper state to initialize " appears 

I have no idea what to do..

I pasted bellow part of the log file and the completed is attached.

Any tip will be welcome!

Thanks a lot :-)

--------------------

P(posterior) = -Infinity (was -Infinity)

P(smcCoalescent) = 703.9708568766605 (was 703.9708568766605)

P(prior) = -Infinity (was -Infinity)

P(BirthDeathCollapseModel.t:Species) = 770.8271685205639 (was 770.8271685205639)

P(bdcGrowthRatePrior.t:Species) = -Infinity (was -Infinity)

P(bdcCollapseWeight.smcTreePrior) = -Infinity (was -Infinity)

P(GammaShapePrior.s:ITS_3M) = -0.39999999999999997 (was -0.39999999999999997)

P(GammaShapePrior.s:MCM7_3M1) = -1.0 (was -1.0)

P(GammaShapePrior.s:RPB1_3M) = -0.39999999999999997 (was -0.39999999999999997)

P(popScalePrior) = -8.849681069015068 (was -8.849681069015068)

P(RateACPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateACPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824)

P(RateACPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateAGPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateAGPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824)

P(RateAGPrior.s:RPB1_Start likelihood: -Infinity after 10 initialisation attempts

3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateATPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateATPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824)

P(RateATPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateCGPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateCGPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824)

P(RateCGPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateCTPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateCTPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824)

P(RateCTPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(RateGTPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824)

P(bdcRelativeDeathRate.smcTreePrior) = -Infinity (was -Infinity)

P(UCMeanRatePrior.c:MCM7_3M1) = -1.0 (was -1.0)

P(UCMeanRatePrior.c:RPB1_3M) = -1.0 (was -1.0)

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.ITS_3M) = NaN (was NaN)  **

P(treeLikelihood.RPB1_3M) = NaN (was NaN)  **

P(treeLikelihood.MCM7_3M1) = NaN (was NaN)  **

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

--------------------------

I attached the xml and log file!

All the best

Alice

u:

[Graham]

Alice,

I don't know why the initialization fails. I had a look at the XML, and saw some things that seemed problematic, but I would expect them to cause problems later, not at initialization.

Site Model: you are estimating all rates in the GTR model for RPB1_3M.

Priors:
You have a normal prior on the bdcGrowthRate, which allows negative values.
You have a prior for popPriorScale which produces values which are much too big. The manual is confusing on this, and I will update it. popPriorScale is a scale for population size *parameters*, roughly speaking, values for N_e mu, not N_e, so typical values for popPriorScale are around 0.001 or 0.01.

With only three loci, and 174 minimal clusters, it is very unlikely you will get useful information about species delimitations.

Graham

[Tim Vaughan]

Hi Alice,

Your analysis doesn't start because your XML specifies upper and lower bounds for some parameters that are not met by their starting values.  The three parameters causing problems are:

1. bdcGrowthRate.  This has an initial value of 50 but has lower bound set to 50 and upper to 10.  You probably want to switch those values around, and increase the upper bound to include 50 (probably a bit above this as you have 50 set to the mean of the corresponding normal prior).

2. relativeDeathRate.  This has an initial value of 0.5 but has upper and lower bounds set to 2.0.

3. collapseWeight.  This has an initial value of 0.5 but has a lower bound of 4 and an upper bound of 2.  So again, the order of the lower and upper bounds needs to be fixed and their values changed to include the starting value.

Fixing these bounds to include the starting values allows the chain to start.  (Example attached, but you should modify it to ensure that the parameter bounds make sense.)

Cheers,

Tim

[Alice Gerlach]

Dear Graham,

WE change the popPriorScale as you suggested and the bdcGrowthRate and after eight run trials the analyses started!

Thank you very much for your useful  tip!

I will tried now with some missing data and the same priors

Then I need try to get better ESS.

Cheers!

Alice

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--

Alice da Cruz Lima Gerlach

Universidade Federal do Rio Grande do Sul (UFRGS)

Instituto de Biociências / Programa de Pós-Graduação em Botânica

Laboratório de Micologia

Av. Bento Gonçalves, 9500 - Campus Vale

CEP 91501-970 - Porto Alegre/RS - Brasil

http://lattes.cnpq.br/3599587053907734

[Alice Gerlach]

Dear Tim

Thank you a lot for your advice.!!

The strange thing is that I used exactly the same prior for a reduced matriy and it worked before.

Cheers,

Alice

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[jonnations]

Hi all,

I am having a problem initializing a run. 355 tips, starting tree, BDP tree model, the goal is to get a time calibrated tree. 

In most of the posts in this thread, there is a discrepancy between prior and "was" value  i.e. P (taxon_set.prior) = X (was Y) 

however I do not see any similar issues in my error message, except for one taxon set starting at "infinity" instead of "NaN". I cannot figure out for the life of me how this taxon set is any different than the others in the xml file. 

If this seems to be a problem with monophyly, I am sorry to waste your time. I checked and rechecked this. I also tried all sets as "monophyletic = "false"" and I got the same message. 

Any help would be greatly appreciated. Thanks!

Jon

Alignment(extant_ingroup)

  355 taxa

  6941 sites

  4679 patterns

Filter 1-2060

355 taxa

2060 sites

1181 patterns

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

  UCRelaxedClockModel: using 708 rate categories to approximate rate distribution across branches.

TreeLikelihood(treeLikelihood.BRCA10) uses BeerLikelihoodCore4

  FilteredAlignment(BRCA1): [taxa, patterns, sites] = [355, 1181, 2060]

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Filter 2061-3012

355 taxa

952 sites

695 patterns

TreeLikelihood(treeLikelihood.GHR0) uses BeerLikelihoodCore4

  FilteredAlignment(GHR): [taxa, patterns, sites] = [355, 695, 952]

Filter 3013-4315

355 taxa

1303 sites

962 patterns

TreeLikelihood(treeLikelihood.IRBP0) uses BeerLikelihoodCore4

  FilteredAlignment(IRBP): [taxa, patterns, sites] = [355, 962, 1303]

Filter 4316-5798

355 taxa

1483 sites

974 patterns

TreeLikelihood(treeLikelihood.RAG10) uses BeerLikelihoodCore4

  FilteredAlignment(RAG1): [taxa, patterns, sites] = [355, 974, 1483]

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Filter 5799-6941

355 taxa

1143 sites

871 patterns

TreeLikelihood(treeLikelihood.CYTB0) uses BeerLikelihoodCore4

  FilteredAlignment(CYTB): [taxa, patterns, sites] = [355, 871, 1143]

===============================================================================

Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA,

  Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian

  evolutionary analysis. PLoS Computational Biology 10(4): e1003537

Gernhard 2008. The conditioned reconstructed process. Journal of Theoretical Biology Volume 253, Issue 4, 21 August 2008, Pages 769-778

Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and

  Dating with Confidence. PLoS Biol 4(5): e88

Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a

  molecular clock of mitochondrial DNA. Journal of Molecular Evolution

  22:160-174.

===============================================================================

Start likelihood: -Infinity after 10 initialisation attempts

P(posterior) = -Infinity (was -Infinity)

P(prior) = -Infinity (was -Infinity)

P(BirthDeath.t:rat_tree) = 602.5827704181186 (was 602.5827704181186)

P(BirthRatePrior.t:rat_tree) = -23.025850929930456 (was -23.025850929930456)

P(GammaShapePrior.s:Subset1) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset2) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset3) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset4) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset5) = -1.0 (was -1.0)

P(KappaPrior.s:Subset3) = -1.8653600339742873 (was -1.8653600339742873)

P(HyperPrior.hyperExponential-mean-10_Rattus_sikkimensis.prior) = -3.7397341883664392 (was -3.7397341883664392)

P(HyperPrior.hyperExponential-mean-11_Leopoldamys_minutus.prior) = -3.6435992933811665 (was -3.6435992933811665)

P(HyperPrior.hyperExponential-mean-12_Leggadina_macrodonta.prior) = -3.7397341883664392 (was -3.7397341883664392)

P(HyperPrior.hyperExponential-mean-13_Chiropodomys_gliroides.prior) = -3.7397341883664392 (was -3.7397341883664392)

P(HyperPrior.hyperExponential-mean-14_Rattus_jaegeri.prior) = -1.8246251312664774 (was -1.8246251312664774)

P(HyperPrior.hyperExponential-mean-15_Zyzomys_rackhami.prior) = -5.160749092237549 (was -5.160749092237549)

P(HyperPrior.hyperExponential-mean-16_Niviventer_preconfucianus.prior) = -2.1508204871617473 (was -2.1508204871617473)

P(HyperPrior.hyperExponential-mean-17_Niviventer_fulvescens.prior) = -0.9959363878291614 (was -0.9959363878291614)

P(HyperPrior.hyperExponential-mean-18_Bandicota_savilei.prior) = -0.9776209369533556 (was -0.9776209369533556)

P(HyperPrior.hyperExponential-mean-19_Bandicota_indica.prior) = -1.0665543445948742 (was -1.0665543445948742)

P(HyperPrior.hyperExponential-mean-1_Antemus.prior) = -7.210823188436418 (was -7.210823188436418)

P(HyperPrior.hyperExponential-mean-20_Berylmys_bowersi.prior) = -0.9776209369533556 (was -0.9776209369533556)

P(HyperPrior.hyperExponential-mean-2_Karnimata_sp.prior) = -7.383705124241564 (was -7.383705124241564)

P(HyperPrior.hyperExponential-mean-3_Apodemus_lugdunensis.prior) = -14.034673295713278 (was -14.034673295713278)

P(HyperPrior.hyperExponential-mean-4_Karnimata_darwini.prior) = -9.628171444018282 (was -9.628171444018282)

P(HyperPrior.hyperExponential-mean-5_Saidomys_sp.prior) = -6.056239963099379 (was -6.056239963099379)

P(HyperPrior.hyperExponential-mean-6_Mus_sp.prior) = -7.98833356110221 (was -7.98833356110221)

P(HyperPrior.hyperExponential-mean-7_Mus_cookii.prior) = -3.0228703373086896 (was -3.0228703373086896)

P(HyperPrior.hyperExponential-mean-8_Pseudomys_vandycki.prior) = -2.270233930369762 (was -2.270233930369762)

P(HyperPrior.hyperExponential-mean-9_Maxomys_surifer.prior) = -3.7397341883664392 (was -3.7397341883664392)

P(PropInvariantPrior.s:Subset2) = 0.0 (was 0.0)

P(PropInvariantPrior.s:Subset3) = 0.0 (was 0.0)

P(PropInvariantPrior.s:Subset4) = 0.0 (was 0.0)

P(PropInvariantPrior.s:Subset5) = 0.0 (was 0.0)

P(RateACPrior.s:Subset1) = -3.184008455701433 (was -3.184008455701433)

P(RateACPrior.s:Subset2) = -3.184008455701433 (was -3.184008455701433)

P(RateACPrior.s:Subset4) = -3.184008455701433 (was -3.184008455701433)

P(RateACPrior.s:Subset5) = -3.184008455701433 (was -3.184008455701433)

P(RateAGPrior.s:Subset1) = -3.1686658147294304 (was -3.1686658147294304)

P(RateAGPrior.s:Subset2) = -3.1686658147294304 (was -3.1686658147294304)

P(RateAGPrior.s:Subset4) = -3.1686658147294304 (was -3.1686658147294304)

P(RateAGPrior.s:Subset5) = -3.1686658147294304 (was -3.1686658147294304)

P(RateATPrior.s:Subset1) = -3.184008455701433 (was -3.184008455701433)

P(RateATPrior.s:Subset2) = -3.184008455701433 (was -3.184008455701433)

P(RateATPrior.s:Subset4) = -3.184008455701433 (was -3.184008455701433)

P(RateATPrior.s:Subset5) = -3.184008455701433 (was -3.184008455701433)

P(RateCGPrior.s:Subset1) = -3.184008455701433 (was -3.184008455701433)

P(RateCGPrior.s:Subset2) = -3.184008455701433 (was -3.184008455701433)

P(RateCGPrior.s:Subset4) = -3.184008455701433 (was -3.184008455701433)

P(RateCGPrior.s:Subset5) = -3.184008455701433 (was -3.184008455701433)

P(RateGTPrior.s:Subset1) = -3.184008455701433 (was -3.184008455701433)

P(RateGTPrior.s:Subset2) = -3.184008455701433 (was -3.184008455701433)

P(RateGTPrior.s:Subset4) = -3.184008455701433 (was -3.184008455701433)

P(RateGTPrior.s:Subset5) = -3.184008455701433 (was -3.184008455701433)

P(DeathRatePrior.t:rat_tree) = 0.0 (was 0.0)

P(MeanRatePrior.c:rat_clock) = -2.402585092994046 (was -2.402585092994046)

P(ucldStdevPrior.c:rat_clock) = 0.819364145120802 (was 0.819364145120802)

P(10_Rattus_sikkimensis.prior) = -Infinity (was -Infinity)

P(11_Leopoldamys_minutus.prior) = NaN (was NaN)  **

P(12_Leggadina_macrodonta.prior) = NaN (was NaN)  **

P(13_Chiropodomys_gliroides.prior) = NaN (was NaN)  **

P(14_Rattus_jaegeri.prior) = NaN (was NaN)  **

P(15_Zyzomys_rackhami.prior) = NaN (was NaN)  **

P(16_Niviventer_preconfucianus.prior) = NaN (was NaN)  **

P(17_Niviventer_fulvescens.prior) = NaN (was NaN)  **

P(18_Bandicota_savilei.prior) = NaN (was NaNFatal exception: Could not find a proper state to initialise. Perhaps try another seed.

)  **

P(19_Bandicota_indica.prior) = NaN (was NaN)  **

P(1_Antemus.prior) = NaN (was NaN)  **

P(20_Berylmys_bowersi.prior) = NaN (was NaN)  **

P(2_Karnimata_sp.prior) = NaN (was NaN)  **

P(3_Apodemus_lugdunensis.prior) = NaN (was NaN)  **

P(4_Karnimata_darwini.prior) = NaN (was NaN)  **

P(5_Saidomys_sp.prior) = NaN (was NaN)  **

P(6_Mus_sp.prior) = NaN (was NaN)  **

P(7_Mus_cookii.prior) = NaN (was NaN)  **

P(8_Pseudomys_vandycki.prior) = NaN (was NaN)  **

P(9_Maxomys_surifer.prior) = NaN (was NaN)  **

[Remco Bouckaert]

Hi Jon,

It is indeed the calibration that becomes infinity causing the problems. The starting tree is very small (perhaps in units of substitutions) but the calibration has an offset of 2.5, so the Rattus_sikkimensis clade in the tree will violate that calibration.

Perhaps you should scale the starting tree so it fits the calibration.

Cheers, 

Remco

By the way, I noticed that many of the means of exponential calibrations are estimated in the XML. Unless you have a really good reason to do this, this probably will hamper convergence, so I would recommend running without estimating these means first.

[jonnations]

Thank you Remco, that was the problem! 

[Tiago Leão]

Dear Remco,

I'm trying to run BEAST2 for an AA alignment of the gene rplB. I built my XML (attached) using the following options:

Site model => Gamma; 

Subst Model => Blosum62.

Clock Model => Relaxed Clock Log Normal.

Priors => Fossilized Birth Death Model, origin 4000;

diversificationRate => Exponential, Mean 1.0;

originFDB => Log Normal, offset 3777 (oldest fossil);

samplingProportionFBD => Beta;

turnoverFBD => Normal;

ucldMean => Exponential, Mean 10.0;

ucldStdev => Gamma

I keep getting the error below, no matter what modifications I do to the XML (I also tried many of the answers above):

===============================================================================

Start likelihood: NaN 

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

P(posterior) = NaN (was NaN)  **

P(prior) = NaN (was NaN)  **

P(FBD.t:L2_fossils) = NaN (was NaN)  **

P(diversificationRatePriorFBD.t:L2_fossils) = -1.0 (was -1.0)

P(originPriorFBD.t:L2_fossils) = -13.421652635441129 (was -13.421652635441129)

P(samplingProportionPriorFBD.t:L2_fossils) = 0.4054651081081638 (was 0.4054651081081638)

P(turnoverPriorFBD.t:L2_fossils) = -1.0439385332046727 (was -1.0439385332046727)

P(MeanRatePrior.c:L2_fossils) = -2.402585092994046 (was -2.402585092994046)

P(ucldStdevPrior.c:L2_fossils) = -3.738879454113936 (was -3.738879454113936)

P(chlorobi.prior) = NaN (was NaN)  **

P(gammasulfurbac.prior) = NaN (was NaN)  **

P(landplants.prior) = NaN (was NaN)  **

P(rhodophyta.prior) = NaN (was NaN)  **

P(tracheophyta.prior) = NaN (was NaN)  **

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.L2_fossils) = NaN (was NaN)  **

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

BEAST has terminated with an error. Please select QUIT from the menu.

Thanks,

Tiago.

[Remco Bouckaert]

Hi Tiago,

The fossilised birth death model can become numerical unstable when ages are large numbers. If you scale the age information to be in thousands of years instead of years, the problem will be solved. So, use 4.0 instead of 4000 for origin age, 3.777 instead of 3777 for oldest fossil offset, etc. 

Also, reduce the population size for the random tree from 1.0 to say 0.1 to get a starting tree that does is smaller than the origin height.

By the way, the alignment has amino acid as datatype, but the substitution model is Jukes Cantor, probably due to a bug in BEAUti. I change it to WAG in the attached XML, but you may want to change it to something more appropriate.The XML should start (perhaps after a few attempts to get a valid starting tree).

Cheers,

Remco

[Tiago Leão]

Hi Remco,

Thank you so much! It did start running after the third attempt.

One last thing, under which tab can I find the option to set the random tree value on BEAUTi? 

I found what line of the XML file can be edited in order to change from 1 to 0.1, however, I am curious if it can be done in BEAUTi as well.

Thanks again,

Tiago.

[tim.ge...@gmail.com]

Hi Remco,

I'm running into this same issue that Tiago had any time I start with an origin age over 250 (even 251). Just out of curiosity, is that an age you would consider to be large enough to make the model unstable?

Thanks,
Tim

[Remco Bouckaert]

Hi Tim,

The problem with the origin age is that the random tree does not take the origin in account, so it may generate a starting tree that is older than the origin. Starting a few times with a different seed can help overcome this problem, but if the population size used in the random tree is too large there may be a high probability of repeatedly generating starting trees that are older than the origin, and then reducing the population size may help.

This problem is not related to the stability of the calculation, which shows up as a birth-death prior being “NaN” (not a number). This is caused by an unfortunate combination of birth/death/sampling rates and branch lengths, and rescaling times say from years to millennia, so that trees become smaller (root age in tens, perhaps hundreds, but not thousands) will solve the problem.

Cheers,

Remco

[Graham]

Perhaps the problem be solved by setting the root height in the random tree? The XML snippet below is from a STACEY analysis, just to illustrate the syntax.

~~~~
    <init id="init:smcTree" spec="RandomTree" estimate="false" taxonset="@taxonSetOfSets" initial="@SMCtree.smctree" rootHeight="0.05">
      <populationModel id="init:smcTree.popmodel" spec="ConstantPopulation">
        <parameter id="init:smcTree:popsize" name="popSize">0.05</parameter>
      </populationModel>
    </init>
~~~~

[Remco Bouckaert]

Good point! That should work with Standard analyses where an origin-parameter is involved as well.

So, if origin height is say 4.01, then adding a rootHeight=“4.0” attribute to the init element with the RandomTree in it should give a starting tree that is less high than the origin height.

[tim.ge...@gmail.com]

Hmm, adding the root height parameter doesn't seem to fix this for some reason. I may be missing something here. I also tried some different population sizes. I'm attaching the my xml file, and here is the stdout:

===============================================================================
Start likelihood: -Infinity after 10 initialisation attempts
P(posterior) = -Infinity (was -Infinity)
    P(prior) = -Infinity (was -Infinity)

        P(FBD.t:snailTree) = -Infinity (was -Infinity)
        P(diversificationRatePriorFBD.t:snailTree) = -1.0 (was -1.0)
        P(originPriorFBD.t:snailTree) = -5.74441889899709 (was -5.74441889899709)
        P(RateACPrior.s:16s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateACPrior.s:28s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateACPrior.s:co1) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateACPrior.s:h3) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateAGPrior.s:16s) = -0.6137056388801093 (was -0.6137056388801093)
        P(RateAGPrior.s:28s) = -0.6137056388801093 (was -0.6137056388801093)
        P(RateAGPrior.s:co1) = -0.6137056388801093 (was -0.6137056388801093)
        P(RateAGPrior.s:h3) = -0.6137056388801093 (was -0.6137056388801093)
        P(RateATPrior.s:16s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateATPrior.s:28s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateATPrior.s:co1) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateATPrior.s:h3) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateCGPrior.s:16s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateCGPrior.s:28s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateCGPrior.s:co1) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateCGPrior.s:h3) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateGTPrior.s:16s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateGTPrior.s:28s) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateGTPrior.s:co1) = -1.2274112777602189 (was -1.2274112777602189)
        P(RateGTPrior.s:h3) = -1.2274112777602189 (was -1.2274112777602189)
        P(samplingProportionPriorFBD.t:snailTree) = 0.4054651081081638 (was 0.4054651081081638)
        P(turnoverPriorFBD.t:snailTree) = 0.0 (was 0.0)
        P(MeanRatePrior.c:snailClock) = -2.402585092994046 (was -2.402585092994046)
        P(ucldStdevPrior.c:snailClock) = 0.7978425306236698 (was 0.7978425306236698)
        P(1_DE_clade.prior) = NaN (was NaN)  **
        P(2_Belau_clade.prior) = NaN (was NaN)  **
        P(3_Cyclophoridae.prior) = NaN (was NaN)  **
        P(4_Pupinidae.prior) = NaN (was NaN)  **
        P(5_Ampullariidae.prior) = NaN (was NaN)  **
        P(6_Viviparidae.prior) = NaN (was NaN)  **
        P(Campanilidae.prior) = NaN (was NaN)  **
        P(Conidae.prior) = NaN (was NaN)  **
        P(Diplo_B.prior) = NaN (was NaN)  **
        P(Diplo_C.prior) = NaN (was NaN)  **
        P(Neocyclotidae.prior) = NaN (was NaN)  **

    P(likelihood) = NaN (was NaN)  **

        P(treeLikelihood.16s_align_fasta) = NaN (was NaN)  **
        P(treeLikelihood.18s_silva_align_fasta) = NaN (was NaN)  **
        P(treeLikelihood.28s_silva_align_edit_fasta) = NaN (was NaN)  **
        P(treeLikelihood.co1_align_fasta) = NaN (was NaN)  **
        P(treeLikelihood.h3_align_fasta) = NaN (was NaN)  **

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.
    at beast.core.MCMC.run(Unknown Source)
    at beast.app.BeastMCMC.run(Unknown Source)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

java.lang.RuntimeException: An error was encounted. Terminating BEAST
    at beast.app.util.ErrorLogHandler.publish(Unknown Source)
    at java.util.logging.Logger.log(Logger.java:738)
    at java.util.logging.Logger.doLog(Logger.java:765)
    at java.util.logging.Logger.log(Logger.java:788)
    at java.util.logging.Logger.severe(Logger.java:1464)

    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)

[Remco Bouckaert]

Hi Tim.

I’m afraid that you have to change units of time so that the SABirthDeathModelproduces finite numbers. Dividing times by 10 will do that.

Cheers,

Remco

<snailFBD_youngorigin.xml>

[Jessica Thomas]

Hi Remco/ all,

I'm new to BEAST and getting the same error message (Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.)

I have a data set of 41 ancient samples and one modern closest living relative. I am starting with strict clock and coalescent constant population. I have set the clock rate and prior information. 

Start likelihood: -Infinity after 10 initialisation attempts

84008455701433 (was -3.184008455701433)

P(GARB.prior) = NaN (was NaN)  **

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.Relaxed_full_withrazorbill_ages_nogaps) = NaN (was NaN)  **

Any ideas? If you need me to post any additional information please let me know!

Cheers,

Jess

[Ángela Celis]

Hi Remco,

I have a problem similar to Jon's problem. I tried to run an analysis for divergence ages estimation in BEAST 2.4.4. on the CIPRES portal using a single nuclear gene, a relaxed molecular clock, an internal calibration point, a maximum age, and a starting tree from RAxML (without node labels).

 

After sending the analysis, I retrieve the following message on the STDOUT document on CIPRES output:

Start likelihood: -Infinity after 10 initialisation attempts

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

And the following message at the STDERR document:

WARNING: the dimension of the parameter is 1 at the start of the run.
        The operator FixMeanMutationRatesOperator has no effect (if this does not change).

P(posterior) = -Infinity (was -Infinity)
    P(prior) = -Infinity (was -Infinity)

        P(YuleModel.t:ITS_20170617_algnMiss) = -96.34901618636 (was -96.34901618636)
        P(YuleBirthRatePrior.t:ITS_20170617_algnMiss) = -1.8862943611198906 (was -1.8862943611198906)
        P(GammaShapePrior.s:ITS_20170617_algnMiss) = -8.294549640102028 (was -8.294549640102028)
        P(RateACPrior.s:ITS_20170617_algnMiss) = -3.184008455701433 (was -3.184008455701433)
        P(RateAGPrior.s:ITS_20170617_algnMiss) = -3.1686658147294304 (was -3.1686658147294304)
        P(RateATPrior.s:ITS_20170617_algnMiss) = -3.184008455701433 (was -3.184008455701433)
        P(RateCGPrior.s:ITS_20170617_algnMiss) = -3.184008455701433 (was -3.184008455701433)
        P(RateGTPrior.s:ITS_20170617_algnMiss) = -3.184008455701433 (was -3.184008455701433)
        P(MeanRatePrior.c:ITS_20170617_algnMiss) = -1.8862943611198906 (was -1.8862943611198906)
        P(ucldStdevPrior.c:ITS_20170617_algnMiss) = 0.819364145120802 (was 0.819364145120802)
        P(MaxAge.prior) = -245.28208743673483 (was -245.28208743673483)
        P(Pmargaritae.prior) = -Infinity (was -Infinity)
    P(likelihood) = NaN (was NaN)  **
        P(treeLikelihood.ITS_20170617_algnMiss) = NaN (was NaN)  **

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.
    at beast.core.MCMC.run(Unknown Source)
    at beast.app.BeastMCMC.run(Unknown Source)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

java.lang.RuntimeException: An error was encounted. Terminating BEAST
    at beast.app.util.ErrorLogHandler.publish(Unknown Source)
    at java.util.logging.Logger.log(Logger.java:738)
    at java.util.logging.Logger.doLog(Logger.java:765)
    at java.util.logging.Logger.log(Logger.java:788)

    at java.util.logging.Logger.severe(Logger.java:1463)

    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)

 

I think that maybe this problem is related to the internal calibration point because in this prior (Pmargaritae.prior) the initialization values goes to infinity. Above, you said to Jon he “should scale the starting tree so it fits the calibration”, so how can I scale the starting tree?

 

Thanks,

Ángela

P.D. I attached the .xml file

[이수랑]

Hello Beast users, 

I ran into similar problem with my run. 

I have read through a couple tutorials and the manual. 

Unfortunately, so far there is no luck for me. 

I am attaching my xml file. Please someone give me some advice on the issue. 

Many thanks in advance. 

2014년 7월 15일 화요일 오전 5시 28분 6초 UTC+9, Norm 님의 말:

Hi, 

I've been having a hard time tracking down the errors when trying to run *BEAST.

The first mistake I had was that not every species was represented in every alignment. I rectified that in a quick and dirty way, by adding a single dummy sequence assigned to each species. Everything else is set according to the *BEAST tutorial. There is a fair amount of missing data in these alignments, since it was from a sequence-capture experiment. I'm just hoping that it's an error in the settings, and not a problem with trying to analyze this particular dataset. 

I will attach the xml. 

Thanks for any advice!

======================================================

Start likelihood: -Infinity after 11 initialisation attempts

P(posterior) = -Infinity (was NaN)

P(speciescoalescent) = -3.3262019264778784E11 (was NaN)

P(SpeciesTreePopSize.Species) = 690.8014759618696 (was NaN)

P(treePrior.t:AT1G01290dum_aln) = -9.642816448055316E10 (was NaN)

P(treePrior.t:AT1G12800dum_aln) = -1.2771911205960396E11 (was NaN)

P(treePrior.t:AT1G18190dum_aln) = -1.0847291679843216E11 (was NaN)

P(prior) = -Infinity (was NaN)

P(YuleModel.t:Species) = 211.30666951105965 (was NaN)

P(YuleBirthRatePrior.t:Species) = -5.362240542149371 (was NaN)

P(ClockPrior.c:AT1G01290dum_aln) = 0.0 (was NaN)

P(ClockPrior.c:AT1G18190dum_aln) = 0.0 (was NaN)

P(KappaPrior.s:AT1G01290dum_aln) = -1.8653600339742873 (was NaN)

P(KappaPrior.s:AT1G12800dum_aln) = -1.8653600339742873 (was NaN)

P(KappaPrior.s:AT1G18190dum_aln) = -1.8653600339742873 (was NaN)

P(popMean.prior) = 0.0 (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.AT1G12800dum_aln) = NaN (was NaN)

P(treeLikelihood.AT1G18190dum_aln) = NaN (was NaN)

P(treeLikelihood.AT1G01290dum_aln) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

[Tim Vaughan]

Hi, there's something wrong with your MRCA prior "Outgroup.prior": the starting tree is resulting in this prior density evaluating to zero.  I'd start looking there.

Tim

[Shook Ling Low]

Hi Beast users,

I faced the similar problem with my run.  

Unfortunately, I couldn't get it solved. 

I am attaching my xml file. Could anyone advice me on this issue? 

Many thanks!

Regards,

SL Low

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[David Černý]

Hi everyone,

Apologies for reviving an old thread, but I'm dealing with the exact same error, and thought posting it here would be better than starting a new one.

I'm trying to date a fixed topology under the "Birth Death Skyline Contemporary BDSParam" tree prior using molecular and morphological data from extant taxa. I'm using BEAST v2.6.3 and BDSKY v1.4.6. I tried to rule out all the potential causes mentioned earlier in this thread or at http://www.beast2.org/2018/07/04/fatal-errors.html, but still wasn't successful in getting the analysis to run:

1. The taxon sets are the same for the molecular partition, the morphological partition, and the starting tree;
2. Unless I'm missing something, the initial values of all parameters are within their respective prior ranges, including the birth and death rates;
3. The MRCA prior taxon sets are all monophyletic, and in any case, setting the monophyletic flag to "false" does not solve the issue;
4. I got my starting tree using the ape::chronos() function in R and checked that the initial heights of all 17 calibrated nodes are compatible with the MRCA priors;
   
5. The heights in the starting tree and in the MRCA priors range from 0 to 50 units, so numerical instability doesn't seem to be the problem, either;
6. The problem persists whether I'm using BEAGLE or disabling it via the -java flag.

My XML is too big to post here, but available at http://drive.google.com/file/d/1QbRUOqKBLbLnmKAN1P4IdSBHfKBbJSRq in case anyone is willing to take a look. Any help would be very much appreciated!

===============================================================================

Start likelihood: NaN 

P(posterior) = NaN (was NaN)  **

P(prior) = NaN (was NaN)  **

P(BirthDeathSkyContemporaryBDSParam.t:morph) = NaN (was NaN)  **

P(birthRatePriorContempBDS.t:morph) = 1.3025850929940455 (was 1.3025850929940455)

P(deathRatePriorContempBDS.t:morph) = 1.3025850929940455 (was 1.3025850929940455)

P(FrequenciesPrior.s:Subset1) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset10) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset11) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset12) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset13) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset14) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset15) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset16) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset17) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset18) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset19) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset2) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset20) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset21) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset22) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset3) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset4) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset5) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset6) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset7) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset8) = 0.0 (was 0.0)

P(FrequenciesPrior.s:Subset9) = 0.0 (was 0.0)

P(GammaShapePrior.s:Subset1) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset10) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset11) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset12) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset13) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset14) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset15) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset16) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset17) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset18) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset19) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset2) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset20) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset21) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset22) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset3) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset4) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset5) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset6) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset7) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset8) = -1.0 (was -1.0)

P(GammaShapePrior.s:Subset9) = -1.0 (was -1.0)

P(GammaShapePrior.s:morph2) = -1.0 (was -1.0)

P(GammaShapePrior.s:morph3) = -1.0 (was -1.0)

P(GammaShapePrior.s:morph4) = -1.0 (was -1.0)

P(GammaShapePrior.s:morph5) = -1.0 (was -1.0)

P(GammaShapePrior.s:morph6) = -1.0 (was -1.0)

P(KappaPrior.s:Subset1) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset10) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset11) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset12) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset13) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset14) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset15) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset16) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset17) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset18) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset19) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset2) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset20) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset21) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset22) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset3) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset4) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset5) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset6) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset7) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset8) = -1.8653600339742873 (was -1.8653600339742873)

P(KappaPrior.s:Subset9) = -1.8653600339742873 (was -1.8653600339742873)

P(MeanRatePrior.c:Subset1) = 4.680075114655892 (was 4.680075114655892)

P(MeanRatePrior.c:morph) = 4.254378833343363 (was 4.254378833343363)

P(ucldStdevPrior.c:Subset1) = 0.8706394709926027 (was 0.8706394709926027)

P(ucldStdevPrior.c:morph) = 0.4931471805599453 (was 0.4931471805599453)

P(Calibration1.prior) = NaN (was NaN)  **

P(Calibration10.prior) = NaN (was NaN)  **

P(Calibration11.prior) = NaN (was NaN)  **

P(Calibration12.prior) = NaN (was NaN)  **

P(Calibration13.prior) = NaN (was NaN)  **

P(Calibration14.prior) = NaN (was NaN)  **

P(Calibration15.prior) = NaN (was NaN)  **

P(Calibration16.prior) = NaN (was NaN)  **

P(Calibration17.prior) = NaN (was NaN)  **

P(Calibration2.prior) = NaN (was NaN)  **

P(Calibration3.prior) = NaN (was NaN)  **

P(Calibration4.prior) = NaN (was NaN)  **

P(Calibration5.prior) = NaN (was NaN)  **

P(Calibration6.prior) = NaN (was NaN)  **

P(Calibration7.prior) = NaN (was NaN)  **

P(Calibration8.prior) = NaN (was NaN)  **

P(Calibration9.prior) = NaN (was NaN)  **

P(likelihood) = NaN (was NaN)  **

P(morphTreeLikelihood.morph2) = NaN (was NaN)  **

P(morphTreeLikelihood.morph3) = NaN (was NaN)  **

P(morphTreeLikelihood.morph4) = NaN (was NaN)  **

P(morphTreeLikelihood.morph5) = NaN (was NaN)  **

P(morphTreeLikelihood.morph6) = NaN (was NaN)  **

P(treeLikelihood.Subset1) = NaN (was NaN)  **

P(treeLikelihood.Subset2) = NaN (was NaN)  **

P(treeLikelihood.Subset3) = NaN (was NaN)  **

P(treeLikelihood.Subset4) = NaN (was NaN)  **

P(treeLikelihood.Subset5) = NaN (was NaN)  **

P(treeLikelihood.Subset6) = NaN (was NaN)  **

P(treeLikelihood.Subset7) = NaN (was NaN)  **

P(treeLikelihood.Subset8) = NaN (was NaN)  **

P(treeLikelihood.Subset9) = NaN (was NaN)  **

P(treeLikelihood.Subset10) = NaN (was NaN)  **

P(treeLikelihood.Subset11) = NaN (was NaN)  **

P(treeLikelihood.Subset12) = NaN (was NaN)  **

P(treeLikelihood.Subset13) = NaN (was NaN)  **

P(treeLikelihood.Subset14) = NaN (was NaN)  **

P(treeLikelihood.Subset15) = NaN (was NaN)  **

P(treeLikelihood.Subset16) = NaN (was NaN)  **

P(treeLikelihood.Subset17) = NaN (was NaN)  **

P(treeLikelihood.Subset18) = NaN (was NaN)  **

P(treeLikelihood.Subset19) = NaN (was NaN)  **

P(treeLikelihood.Subset20) = NaN (was NaN)  **

P(treeLikelihood.Subset21) = NaN (was NaN)  **

P(treeLikelihood.Subset22) = NaN (was NaN)  **

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.

See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

java.lang.RuntimeException: An error was encounted. Terminating BEAST

at beast.app.util.ErrorLogHandler.publish(Unknown Source)

at java.util.logging.Logger.log(Logger.java:738)

at java.util.logging.Logger.doLog(Logger.java:765)

at java.util.logging.Logger.log(Logger.java:788)

at java.util.logging.Logger.severe(Logger.java:1464)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

[Carol Adam]

Hey guys!

I'm trying to estimate divergence times for three species using SNP data. I set two monophyletic constraints and calibration points.

I've been reading multiple threads on the matter and tried many fixes,  this thread is really helpful, but I'm still banging my head against the wall and cannot make the analysis to run.

Here is the link for my XML file, and the relevant screen log info is below.

Any insights on the matter will be much appreciated.

Cheers,

~Carol.

Start likelihood: -Infinity after 10 initialisation attempts

P(posterior) = -Infinity (was -Infinity)

P(prior) = -Infinity (was -Infinity)

P(lambdaPrior.snps_nomissing_bin_with_outgroup) = -17.50444001207821 (was -17.50444001207821)

P(snapprior.snps_nomissing_bin_with_outgroup) = -70.0888438514922 (was -70.0888438514922)

P(fragum.prior) = -Infinity (was -Infinity)

P(root.prior) = NaN (was NaN)  **

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.snps_nomissing_bin_with_outgroup) = NaN (was NaN)  **

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.

See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.base/java.lang.reflect.Method.invoke(Method.java:566)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

java.lang.RuntimeException: An error was encounted. Terminating BEAST

at beast.app.util.ErrorLogHandler.publish(Unknown Source)

at java.logging/java.util.logging.Logger.log(Logger.java:979)

at java.logging/java.util.logging.Logger.doLog(Logger.java:1006)

at java.logging/java.util.logging.Logger.log(Logger.java:1029)

at java.logging/java.util.logging.Logger.severe(Logger.java:1776)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.base/java.lang.reflect.Method.invoke(Method.java:566)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)