MLE- Path sampling
Şener Ulu
Hi there,
I’m new to the BEAST platform and would greatly appreciate any help with the following issue.
I'm trying to estimate the marginal likelihood of a phylogeny set up with StarBEAST3 template in BEAST v2.7.7. The regular StarBEAST3 .xml file runs successfully and produces reasonable results. However, when I attempt to perform marginal likelihood estimation of this phylogeny via path sampling, the modified .xml file crashes.
I manually edited the .xml file following the instructions at www.beast2.org/path-sampling, but so far none of my attempts have worked. I've tried running the file both locally and on the CIPRES portal, but none of them has been successful.
When I run it locally, the process generates the step* folders and run.sh outputs, but nothing else happens afterward. Below is an example of the error I consistently receive. I also tried suggestions found in a chat regarding "error with BEAST2.2.0 SNAPP+MODEL_SELECTION", but they didn’t resolve the issue.
Thanks a lot for any insights or advice !
Loading package CCD v1.0.0
Loading package SA v2.1.1
Loading package BEAST.base v2.7.7
Loading package BEASTLabs v2.0.2
Loading package BEAST.app v2.7.7
Loading package ORC v1.2.0
Loading package STACEY v1.3.1
Loading package MODEL_SELECTION v1.6.2
/Users/Sener/Desktop/RECOMBINATION_WORK/PATHSAMPLING/RC_pathsampling/step0/run.sh
Error: Could not find or load main class beast.pkgmgmt.launcher.BeastLauncher
Caused by: java.lang.ClassNotFoundException: beast.pkgmgmt.launcher.BeastLauncher
java.io.FileNotFoundException: /Users/Sener/Desktop/RECOMBINATION_WORK/PATHSAMPLING/RC_pathsampling/step0/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.Controller$2.run(Unknown Source)