search

genomescale / starbeast2

Faster multispecies coalescent inference using multilocus data
GNU Lesser General Public License v2.1
13 stars 5 forks source link

*beast2RLC: Fatal exception based on incomplete taxon representation #16

Closed rbouckaert closed 6 years ago

rbouckaert commented 6 years ago

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)

genomescale commented 6 years ago

This is fixed in version 0.14, thanks for transferring the issue over to the right repo @rbouckaert

mariaemilyd commented 4 years ago

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.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at beast.app.beastapp.BeastLauncher.run(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source) 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

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

Thanks!

genomescale commented 4 years ago

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