SNAPPER Stepping Stone Analysis for species delimitation with BFD not working

[Corné van der Linden]

Hi all,

I am trying to get a SNAPPER stepping stone analysis set up for species delimitation, but I cannot seem to get it running.

When I run my xml it makes all the output directories but there are no .state or .log files being produced and then it gives the following error:

java.io.FileNotFoundException: /home/BFD_snapper/4_species/run1_test/step15/beast.xml.state (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(Unknown Source)
at java.base/java.io.FileInputStream.<init>(Unknown Source)
at modelselection.inference.PathSampler.copyStateFile(Unknown Source)
at modelselection.inference.PathSampler.doRuns(Unknown Source)
at modelselection.inference.PathSampler.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.BeastMain.main(Unknown Source)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at beast.pkgmgmt.launcher.BeastLauncher.run(Unknown Source)
at beast.pkgmgmt.launcher.BeastLauncher.main(Unknown Source)

SNAPPER works by itself and so does speedemon.

I also don't think that Java seems to be the problem.

java -version
openjdk version "11.0.25" 2024-10-15

Any help would be greatly appreciated!

Greetings, 

from Corné

[Omar Idris]

beast /path/to/yourfile.xml

If on command line. I have solved this issue in gui but can exactly remember what caused it I suspect it is incorrect xml.

Sent from my iPhone

On Feb 12, 2025, at 2:12 PM, Corné van der Linden <cornevand...@gmail.com> wrote:



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