Is it normal that pop up a dialog box and let me to choose xml file?

[liamxg]

Dear @tgvaughan, When I run run_analyses.sh, it pops up a dialog box and let me to choose xml file, is that normal?

[liamxg]

[tgvaughan]

Hi Liam, no this is not normal. May I ask what operating system you are using?

[liamxg]

[liamxg]

Hi @tgvaughan, I use MAC OS.

[tgvaughan]

Have you edited the script at all? It sounds like beast is being run with an empty file argument.

[liamxg]

[tgvaughan]

Unfortunately your edited script is not correct: you'll need to use the standard beast launch script (named beast, as in the original file) to run beast. If this is not already in your execution path, you can add its full path to the script. It should be found in the bin/ subdirectory of your beast installation directory.

[liamxg]

                   BEAST v2.7.6, 2002-2023
         Bayesian Evolutionary Analysis Sampling Trees
                   Designed and developed by

Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

               Centre for Computational Evolution
                     University of Auckland
                   r.bouckaert@auckland.ac.nz
                    alexei@cs.auckland.ac.nz

               Institute of Evolutionary Biology
                    University of Edinburgh
                       a.rambaut@ed.ac.uk

                David Geffen School of Medicine
             University of California, Los Angeles
                       msuchard@ucla.edu

                  Downloads, Help & Resources:
                       http://beast2.org/

Source code distributed under the GNU Lesser General Public License: http://github.com/CompEvol/beast2

                       BEAST developers:

Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie

                           Thanks to:
      Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Writing state to file Results/TrajectoryMapper.10.state Random number seed: 10

File: TrajectoryMapper.xml seed: 10 threads: 1 Loading package BICEPS v1.1.1 SSM v1.2.0 ClaDS v2.0.2 contraband v1.0.1 FastRelaxedClockLogNormal v1.2.0 MGSM v0.4.0 feast v9.4.0 phylodynamics v1.4.0 BADTRIP v2.0.0 NS v1.2.0 bModelTest v1.3.3 BASTA v4.0.0 CA v2.1.0 LPhyBeastExt v0.2.0 speedemon v1.1.0 starbeast3 v1.1.7 SpeciesNetwork v1.0.0 timtam v0.4.0 Mascot v3.0.0 PhyDyn v1.4.0 PIQMEE v1.1.0 phylonco v1.0.0 starbeast2 v1.0.0 TreeStat2 v0.1.1 MSBD v2.0.1 Babel v0.4.1 SA v2.1.1 BEAST.base v2.7.6 MultiTypeTree v8.0.0 BDMM v2.0.0 GEO_SPHERE v1.4.1 MASTER v7.0.0 DENIM v1.1.1 BEASTLabs v2.0.0 BEAST.app v2.7.6 BEAST_CLASSIC v1.6.2 CodonSubstModels v2.0.0 MM v1.2.1 CoupledMCMC v1.2.0 BDSKY v1.5.0 OBAMA v1.1.1 bdtree v0.0.1 snapper v1.1.2 SCOTTI v3.0.0 ORC v1.1.1 SNAPP v1.6.1 Recombination v1.0.1 STACEY v1.3.1 BREAK_AWAY v1.2.0 MODEL_SELECTION v1.6.1 lphybeast v1.0.1 CoalRe v1.0.3 bacter v3.0.1 BEASTvntr v0.2.0 EpiInf v8.0.0

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.base.inference.parameter.RealParameter? Perhaps a package required for this class is not installed?

Error detected about here:

[liamxg]

Hi, @tgvaughan,

I guess it's almost time to run.

[tgvaughan]

Ah, this is the wrong beast 2 version: you'll need 2.6.7 to run these analyses.

[liamxg]

                    BEAST v2.6.7, 2002-2022
         Bayesian Evolutionary Analysis Sampling Trees
                   Designed and developed by

Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

               Centre for Computational Evolution
                     University of Auckland
                   r.bouckaert@auckland.ac.nz
                    alexei@cs.auckland.ac.nz

               Institute of Evolutionary Biology
                    University of Edinburgh
                       a.rambaut@ed.ac.uk

                David Geffen School of Medicine
             University of California, Los Angeles
                       msuchard@ucla.edu

                  Downloads, Help & Resources:
                       http://beast2.org/

Source code distributed under the GNU Lesser General Public License: http://github.com/CompEvol/beast2

                       BEAST developers:

Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie

                           Thanks to:
      Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Writing state to file Results/BD_indep_noseq.3.state Random number seed: 3

File: BD_indep_noseq.xml seed: 3 threads: 1 Loading package BEAST v2.6.7 Loading package feast v8.4.0 Loading package BDMM-Prime v0.0.24 Loading package SA v2.0.2 Loading package BEASTLabs v1.9.7 Loading package BDSKY v1.4.8 Loading package Recombination v0.0.2 Loading package CoalRe v0.0.7 Loading package EpiInf v7.5.2

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.evolution.tree.TreeHeightLogger? Perhaps a package required for this class is not installed?

Error detected about here:

[liamxg]

Hi @tgvaughan, When I change beast from version 2.7.6 to 2.6.7, it still has error as above.

[tgvaughan]

Hi Liam, it seems there's one extra dependency - sorry! I've added it to the readme now. You'll need to also have the MultiTypeTree package installed. (The error you pasted above points this out, although github has rendered this invisible.)

[liamxg]

Dear @tgvaughan, Thanks for you tips.