BEAST 2 package MultiTypeTree tutorial problems

[Ana Bento]

HI,

I was trying to run this  tutorial (https://github.com/tgvaughan/MultiTypeTree/wiki/Beginner's-Tutorial-(short-version)

Using the data from the working directory and following the tutorial instructions but i get an error when i upload the saved xml file i create on beauti (attached). Im also attaching a screenshot of what i input, since my beauti options are different from the screenshots in your tutorial. Can you help me?

I want to use my own data for B pertussis, but i wanted to have it run with your data first.

Thanks so much!

Ana

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

Start likelihood: -Infinity after 10 initialisation attempts

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

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

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

P(birthDeathMigration.t:h3n2_2deme) = -Infinity (was -Infinity)

P(RPrior.t:h3n2_2deme) = -3.7046244414474376 (was -3.7046244414474376)

P(becomeUninfectiousRatePrior.t:h3n2_2deme) = -1.8378770664093453 (was -1.8378770664093453)

P(KappaPrior.s:h3n2_2deme) = -1.8653600339742873 (was -1.8653600339742873)

P(rateMatrixPrior.t:h3n2_2deme) = -2.1294214739848565 (was -2.1294214739848565)

P(samplingProportionPrior.t:h3n2_2deme) = 1.7763568394002497E-15 (was 1.7763568394002497E-15)

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.h3n2_2deme) = 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.

[Tim Vaughan]

Dear Ana, thanks for getting in touch.  From your screenshot it seems you are in fact using the MultiTypeBirthDeath (BDMM) BEAUti template, not the MultiTypeTree template.  The instructions at the start of the tutorial indicate how to use the correct template.  You'll know it's correct because the options you see will match the screenshots in the tutorial.

Best of luck!

Tim

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