Closed rbouckaert closed 6 years ago
This is fixed in version 0.14, thanks for transferring the issue over to the right repo @rbouckaert
Hi there, I'm getting the same error message that not all taxa are represented in every gene alignment. I'm using StarBEAST v 0.15.5 and BEAST v2.6.0:
Fatal exception: Gene tree Tree.t:O_rosmarus_Lindqvist_2016_NADH_all_aligned_seq_27_11_2018 has no lineages for species taxon Eastern_Laptev
java.lang.RuntimeException: Gene tree Tree.t:O_rosmarus_Lindqvist_2016_NADH_all_aligned_seq_27_11_2018 has no lineages for species taxon Eastern_Laptev
at beast.evolution.speciation.StarBeastStartState.fullInit(Unknown Source)
at beast.evolution.speciation.StarBeastStartState.initStateNodes(Unknown Source)
at beast.core.MCMC.run(Unknown Source)
at beast.app.BeastMCMC.run(Unknown Source)
at beast.app.beastapp.BeastMain.
BEAST has terminated with an error. Please select QUIT from the menu.
Thanks!
Hi Maria, this is the old *BEAST implementation, to be able to run an analysis with missing data you should use one of the StarBEAST2 templates (see the StarBEAST2 tutorial for details)
Regards,
Huw
This was submitted as a BEAST 2 issue #715, but I think this is a SartBEAST2 issue.
Hi there,
I'm trying to run *beast2RLC with 60 odd gene trees and up to 24 taxa. Looks like the problem is that not all taxa are represented in every gene alignment.
Test dataset with *beast2 RLC template worked fine previously, at that point taxa were represented in all gene alignments. Ran on Linux based cluster as well as Ubuntu OS laptop - this error is coming up for both systems now.
Is there a way to make this run without screening which taxa are missing in each gene alignment and then adding gaps? Thanks!
StarBEAST2: using fullInit to initialize all trees. Fatal exception: Gene tree Tree.t:EPrGT00050000005290 has no lineages for species taxon ALEXANDRIUM-CATENELLA java.lang.RuntimeException: Gene tree Tree.t:EPrGT00050000005290 has no lineages for species taxon ALEXANDRIUM-CATENELLA at starbeast2.StarBeastInitializer.fullInit(StarBeastInitializer.java:246) at starbeast2.StarBeastInitializer.initStateNodes(StarBeastInitializer.java:101) at beast.core.MCMC.run(Unknown Source) at beast.app.BeastMCMC.run(Unknown Source) at beast.app.beastapp.BeastMain.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source) Fatal exception: Gene tree Tree.t:EPrGT00050000005290 has no lineages for species taxon ALEXANDRIUM-CATENELLA 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.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source)