Problems in running Stacey in BEAST2 in Linux system

[francisco fonseca ribeiro de oliveira]

Dear folks,

I'm trying to run a STACEY analysis in BEAST 2, but when I load the "xml" file (already configured in the Stacey template) and run BEAST 2, the following error message appears:

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)

I put the executable "Stacey.jar" file in the same diretory as the executable "Beast 2.jar" (considering that I'm running it in Linux).

There seems to be a problem in the configuration of the MCMC run. I'm running it with a chain length of 250.000.000, sampling every 25.000 and with a pre-burnin of 100.000.000.

Any help would be appreciated.

Thank you.

[bander...@gmail.com]

I haven't used STACEY, but perhaps you could try giving BEAST a starting tree that matches the constraints you may have given it (?). (or adjusting priors to be less restrictive?)

I encountered a similar error in a divergence time estimation. The only solution I found was to give it a tree that had branch lengths for a node close to where I put my most restrictive fossil calibration. Interestingly, adjusting that calibration to make it younger by only 5 million years and BEAST had no problem with a random tree.