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R package to run BEAST2

Home Page: https://docs.ropensci.org/beastier

License: GNU General Public License v3.0

R 97.54% Shell 1.38% Singularity 1.08%

r r-package rstats bayesian beast beast2 phylogenetic-inference phylogenetics

beastier's Introduction

beastier

Branch
`master`
`develop`

beastier is an R package to run BEAST2.

beastier is part of the babette package suite:

beautier creates BEAST2 input (.xml) files.
beastier runs BEAST2
mauricer: install BEAST2 packages
tracerer pastes BEAST2 output (.log, .trees, etc) files.

Related R packages:

beastierinstall: Install and uninstall BEAST2
beastier_on_windows: Verify that beastier works on the Windows operating system
lumier: Shiny app to help create the function call needed

Install BEAST2

Due to CRAN policy, beastier cannot install BEAST2. As a workaround, the non-CRAN beastierinstall can be used.

To install BEAST2:

remotes::install_github("richelbilderbeek/beastierinstall")
beastierinstall::install_beast2()

Example for `v2.1`

Run BEAST2:

output_state_filename <- "out.state"

run_beast2(
  input_filename = get_beastier_path("2_4.xml"),
  output_state_filename = output_state_filename
)

This will create the files as specified in the 2_4.xml BEAST2 input file.

Example for `v2.0.25`

output_log_filename <- "out.log"
output_trees_filename <- "out.trees"
output_state_filename <- "out.state"

run_beast2(
  input_filename = get_beastier_path("2_4.xml"),
  output_log_filename = output_log_filename,
  output_trees_filenames = output_trees_filename,
  output_state_filename = output_state_filename
)

Note that in this version, the filenames for the .log and .trees files could be specified. This is unneeded: the 2_4.xml BEAST2 input file specifies where these files will be stored:

<?xml [...]?><beast [...]>

[...]

<run [...]>

    [...]

    <logger id="tracelog" fileName="test_output_0.log" [...]>
        [...]
    </logger>

    [...]

    <logger id="treelog.t:[...]" fileName="$(tree).trees" [...]>
        [...]
    </logger>
</run>
</beast>

When using beautier, this can be specified in create_mcmc:

create_mcmc(
  tracelog = create_tracelog(
    filename = "my_trace.log"
  ),
  treeslog = create_treeslog(
    filename = "my_trees.trees"
  )
)

Install

See install.

FAQ

See FAQ

Missing features/unsupported

beastier cannot do everything BEAST2 can.

Remove: install BEAST2, use beastierinstall
Experimental: Continue a BEAST2 run
Untested: Setup BEAGLE

There is a feature I miss

See CONTRIBUTING, at Submitting use cases

I want to collaborate

See CONTRIBUTING, at 'Submitting code'

I think I have found a bug

See CONTRIBUTING, at 'Submitting bugs'

There's something else I want to say

Sure, just add an Issue. Or send an email.

External links

BEAST2 GitHub

Dependencies

Branch
`beautier` `master`
`beautier` `develop`
`beastierinstall` `master`
`beastierinstall` `develop`

Branch
`beastier_on_windows` `master`
`beastier_on_windows` `develop`

References

Article about babette:

Bilderbeek, Richèl JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032

FASTA files anthus_aco.fas and anthus_nd2.fas from:

Van Els, Paul, and Heraldo V. Norambuena. "A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data." Ibis.

beastier's People

Contributors

Stargazers

Watchers

Forkers

giappo olivroy

beastier's Issues

Forbidden to download from https://github.com on CARL cluster

[edit by @richelbilderbeek: this Issue had nothing to do with beastier]

On a cluster (not peregrine), beastier::install_beast2 fails with:

downloaded 0 bytes

Error in utils::download.file(url = url, destfile = local_path) : 
  cannot download all files
In addition: Warning message:
In utils::download.file(url = url, destfile = local_path) :
  URL 'https://github-production-release-asset-2e65be.s3.amazonaws.com/15949777/195f6580-2aaa-11e9-9ba5-3f6739d075c1?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20190603%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20190603T084329Z&X-Amz-Expires=300&X-Amz-Signature=4835b41670df45c54f9e07df88a37b62212f1903dcf942cd5d7c3b2302aa4605&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DBEAST.v2.5.2.Linux.tgz&response-content-type=application%2Foctet-stream': status was '403 Forbidden'

Idea: run BEAST2 in temporary folder?

Currently, BEAST2 is run in the working directory of the user, after which files are moved to temporary paths.

Perhaps using a temporary folder for BEAST2 simplifies things a lot.

beastier is not silent under Windows

Redirected from this Issue to here, as beastier causes the unnecessarily verbose output on Windows.

Tip dates functionality?

Great resource! Do you have plans for a function to import tip dates?
Thank you!

gives_beast2_warning documentation should link to is_beast2_input_file

Feedback bjoelle:

gives_beast2_warning: this doc should link to is_beast2_input_file rather than are_beast2_input_lines since the input is a file in both.

BEAST2 .log file not created

Thanks @thijsjanzen for the bug report!

Re: BEAST op het cluster: nogmaalser

9 August 2019 14:22 111 KB
From: Janzen, T.
Met VERBOSE = TRUE:

inferring alternative trees

/data/p251362/nodeSub/no_extinct/shared/7 

working dir updated to: 

/home/p251362/.cache/file1d8d62a4db8a/7 

[1] "input_filename: /local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml"

[1] "output_log_filename: alternative.log"

[1] "output_trees_filenames: alternative.trees"

[1] "output_state_filename: /local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state"

 [1] ""                                                                                

 [2] "                        BEAST v2.6.0, 2002-2019"                                 

 [3] "             Bayesian Evolutionary Analysis Sampling Trees"                      

 [4] "                       Designed and developed by"                                

 [5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"          

 [6] "                                    "                                            

 [7] "                   Centre for Computational Evolution"                           

 [8] "                         University of Auckland"                                 

 [9] "                       [email protected]"                               

[10] "                        [email protected]"                                

[11] "                                    "                                            

[12] "                   Institute of Evolutionary Biology"                            

[13] "                        University of Edinburgh"                                 

[14] "                           [email protected]"                                   

[15] "                                    "                                            

[16] "                    David Geffen School of Medicine"                             

[17] "                 University of California, Los Angeles"                          

[18] "                           [email protected]"                                    

[19] "                                    "                                            

[20] "                      Downloads, Help & Resources:"                              

[21] "                           http://beast2.org/"                                   

[22] "                                    "                                            

[23] "  Source code distributed under the GNU Lesser General Public License:"          

[24] "                   http://github.com/CompEvol/beast2"                            

[25] "                                    "                                            

[26] "                           BEAST developers:"                                    

[27] "   Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "            

[28] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "          

[29] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "        

[30] "          Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"                   

[31] "                                    "                                            

[32] "                               Thanks to:"                                       

[33] "          Roald Forsberg, Beth Shapiro and Korbinian Strimmer"                   

[34] ""                                                                                

[35] "Random number seed: 1565352693439"                                               

[36] ""                                                                                

[37] "File: file1d8d66a637bd7.xml seed: 1565352693439 threads: 1"                      

[38] "Loading package BEAST v2.6.0"                                                    

[39] "Loading package BEAST v2.6.0"                                                    

[40] "Alignment(temp)"                                                                 

[41] "  100 taxa"                                                                      

[42] "  1000 sites"                                                                    

[43] "  1000 patterns"                                                                 

[44] ""                                                                                

[45] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"            

[46] "TreeLikelihood(treeLikelihood.temp0) uses BeerLikelihoodCore4"                   

[47] "  Alignment(temp): [taxa, patterns, sites] = [100, 1000, 1000]"                  

[48] "===============================================================================" 

[49] "Citations for this model:"                                                       

[50] ""                                                                                

[51] "Bouckaert, Remco, Timothy G. Vaughan, JoÃ«lle Barido-Sottani, SebastiÃ¡n DuchÃªne, "

[52] "  Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "                

[53] "  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. " 

[54] "  PLoS computational biology 15, no. 4 (2019): e1006650."                        

[55] ""                                                                                

[56] "===============================================================================" 

[57] "Done!"                                                                           

[1] "input_filename_full: /local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml"

[1] "actual_log_filename: /home/p251362/.cache/file1d8d62a4db8a/7/temp.log"

[1] "actual_trees_filenames: /home/p251362/.cache/file1d8d62a4db8a/7/temp.trees"

[1] "output_log_filename_full: /data/p251362/nodeSub/no_extinct/shared/7/alternative.log"

[1] "output_trees_filenames_full: /data/p251362/nodeSub/no_extinct/shared/7/alternative.trees"

[1] "output_state_filename_full: /local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state"

 [1] ""                                                                                

 [2] "                        BEAST v2.6.0, 2002-2019"                                 

 [3] "             Bayesian Evolutionary Analysis Sampling Trees"                      

 [4] "                       Designed and developed by"                                

 [5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"          

 [6] "                                    "                                            

 [7] "                   Centre for Computational Evolution"                           

 [8] "                         University of Auckland"                                 

 [9] "                       [email protected]"                               

[10] "                        [email protected]"                                

[11] "                                    "                                            

[12] "                   Institute of Evolutionary Biology"                            

[13] "                        University of Edinburgh"                                 

[14] "                           [email protected]"                                   

[15] "                                    "                                            

[16] "                    David Geffen School of Medicine"                             

[17] "                 University of California, Los Angeles"                          

[18] "                           [email protected]"                                    

[19] "                                    "                                            

[20] "                      Downloads, Help & Resources:"                              

[21] "                           http://beast2.org/"                                   

[22] "                                    "                                            

[23] "  Source code distributed under the GNU Lesser General Public License:"          

[24] "                   http://github.com/CompEvol/beast2"                            

[25] "                                    "                                            

[26] "                           BEAST developers:"                                    

[27] "   Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "            

[28] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "          

[29] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "        

[30] "          Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"                   

[31] "                                    "                                            

[32] "                               Thanks to:"                                       

[33] "          Roald Forsberg, Beth Shapiro and Korbinian Strimmer"                   

[34] ""                                                                                

[35] "Random number seed: 1565352696500"                                               

[36] ""                                                                                

[37] "File: file1d8d66a637bd7.xml seed: 1565352696500 threads: 1"                      

[38] "Loading package BEAST v2.6.0"                                                    

[39] "Loading package BEAST v2.6.0"                                                    

[40] "Alignment(temp)"                                                                 

[41] "  100 taxa"                                                                      

[42] "  1000 sites"                                                                    

[43] "  1000 patterns"                                                                 

[44] ""                                                                                

[45] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"            

[46] "TreeLikelihood(treeLikelihood.temp0) uses BeerLikelihoodCore4"                   

[47] "  Alignment(temp): [taxa, patterns, sites] = [100, 1000, 1000]"                  

[48] "===============================================================================" 

[49] "Citations for this model:"                                                       

[50] ""                                                                                

[51] "Bouckaert, Remco, Timothy G. Vaughan, JoÃ«lle Barido-Sottani, SebastiÃ¡n DuchÃªne, "

[52] "  Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "                

[53] "  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. " 

[54] "  PLoS computational biology 15, no. 4 (2019): e1006650."                        

[55] ""                                                                                

[56] "===============================================================================" 

[57] "Done!"                                                                           

[1] "cmd: /apps/generic/software/Java/1.8.0_192/jre/bin/java -jar '/home/p251362/.local/share/beast/lib/launcher.jar' -seed 1565352623.58915 -statefile \"/local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state\" -overwrite \"/local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml\""

Error in beastier::run_beast2(input_filename = beast2_input_filename,  : 

  BEAST2 .log file not created at '/home/p251362/.cache/file1d8d62a4db8a/7/temp.log' 

Maybe no permission to write at that location?

Calls: infer_phylogeny -> <Anonymous> -> bbt_run -> <Anonymous>

In addition: Warning messages:

1: In regularize.values(x, y, ties, missing(ties)) :

  collapsing to unique 'x' values

2: In system2(command = cmd[1], args = cmd[-1], stdout = TRUE, stderr = TRUE) :

  running command ''/apps/generic/software/Java/1.8.0_192/jre/bin/java' -jar '/home/p251362/.local/share/beast/lib/launcher.jar' -seed 1565352623.58915 -statefile "/local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state" -overwrite "/local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml" 2>&1' had status 1

Execution halted

Explore to run BEAST2 from temp folder

Currently, beastier has some special file handling, due to BEAST2's file creation. This would maybe vanish if BEAST2 was run run with pwd set to a temp folder.

Document that 'has_unique_ids' only checks real parameters

Feedback bjoelle:

has_unique_ids: the doc of this function implies that it checks both parameter and distribution ids, but get_duplicate_ids only checks real parameters

Pass CRAN CI

From :

* checking examples ... ERROR
Running examples in ‘beastier-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_default_log_filename
> ### Title: Create the default '.log' filename as will be created by BEAST
> ### Aliases: create_default_log_filename
> 
> ### ** Examples
> 
>   library(testthat)
> 
>   input_filename <- get_beastier_path("2_4.xml")
>   log_filename <- create_default_log_filename(input_filename)
Error in check_beast2_path(beast2_path) : 
  'beast2_path' must be the name of an existing file. File '/home/hornik/.local/share/beast/lib/beast.jar' not found
Calls: create_default_log_filename -> check_beast2_path
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE

Clear: there is no BEAST2 installed on the CRAN CI, run Travis without installing it...

is_beast2_input_file should suppress warnings

  beastier::is_beast2_input_file(
    mauricer::get_mrc_path("nested_sampling.xml"),
    show_warnings = FALSE
  )

Bug reminder

(No subject)

2 November 2018 17:10 3 KB
From:
Rivera Leon, V.E.
To: [...]

Fx pease

https://github.com/richelbilderbeek/beastier/blob/3c9a43fa58df11133b3d9417b93800ad40ee5e59/R/is_beast2_input_file.R#L40

Implement feedback CRAN

Re: CRAN submission beastier 2.0.13

23 May 2019 11:56 9 KB
From:
Uwe Ligges
To:
Richèl J.C. Bilderbeek, CRAN

Thanks, can you please add a
SystemRequirements field to the DESCRIPTION file and define BEAST2 (and if applicable a minimal version) that you package apparently needs?

Please fix and resubmit.

Best,
Uwe Ligges

Fix script install_beast2 on Mac

Fails due to sed having another user interface on Mac

create_posterior should be used or removed

Feedback bjoelle:

create_posterior: it's unclear what this function is meant to be used for, as it's not exported or called from anywhere else in the package

Update BEAST2

Write beastier::update_beast2() to update the current version of BEAST2

Invalid cross-device link

Error: file.exists(output_log_filename) is not TRUE
In addition: Warning messages:
1: In file.rename(from = from, to = output_log_filename) :
  cannot rename file 'test_output_0.log' to '/tmp/RtmpCkIwGP/file1ef65a706c8.log', reason 'Invalid cross-device link'
2: In file.rename(from = from, to = to) :

Add 'upgrade_beast2'

For older user that need to update.

Get beastier at rOpenSci

Create an Issue at rOpenSci

run_beast2 should or should not overwrite the correct file

Feedback bjoelle:

run_beast2, create_beast2_run_cmd: the -overwrite option for BEAST2 is not for overwriting the state file (it will always be overwritten), it is for overwriting the log & trees files. Thus at the moment setting overwrite_state_file does nothing (it's also always set back to TRUE at l107 in run_beast2).

beastier must run on Windows

Created beastier_on_windows repo.

Process CRAN feedback

From Martina Schmirl:

please omit the redundant "from R" in the title.

Done

please omit double spaces in the description (e.g. "'BEAST2' from").

Done, replaced all double spaces by four spaces

Please always write package names, software names and API names in single quotes (e.g. 'BEAST2', 'R') in the title and the description field.

Done.

The LICENSE file is only needed if you have additional restrictions to the GPL-3 which you have not? In that case omit the file and its reference in the DESCRIPTION file.

Done.

Please provide small executable examples in all your exported functions' Rd files to illustrate the use of the exported function but also enable automatic testing.

Done. Thanks for spotting this, I think this is important myself, but somehow overlooked it.

Please fix and resubmit.

TODO

run_beast2 should document what a seed of NA does

Feedback bjoelle:

run_beast2, create_beast2_run_cmd: the doc should mention that rng_seed can be NA and what happens in that case (i.e the seed will be set to random).

Add 'beastier_self_test'

Uses do_minimal_run someway.

Build under MacOSX

See here.

Current problem is:

The command "sudo apt-get install -qq oracle-java8-installer" failed and exited with 1 during

Add 'beast2_options' parameter struct

Check if citation works

Get BEAST2 version

An informal request by @thijsjanzen:

Write beastier::get_beast2_version() to obtain the BEAST2 version

Add 'update_beastier`

Calls remote::install_github on all beastier friends, which are tracerer and beautier

Store BEAST2 input (.xml) filename in beast2_options

Need it for mcbette

Add: 'delete_beast2_files(beast2_options)'

Fix CRAN build note: Author field differs from that derived from Authors@R

From CRAN build log:

* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Richèl J.C. Bilderbeek <[email protected]>’
  Authors@R: ‘Richèl J.C. Bilderbeek [aut, cre] (<https://orcid.org/0000-0003-1107-7049>), Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209), David Winter [rev] (David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209)’

Allow using BEAST2's example NEXUS and XML files

In ~/.local/share/beast/examples/nexus/ are NEXUS files, in its superfolder XML files.

Create a function get_beast2_example_filenames() that returns a list of the full path to the BEAST2 example filenames
Create a function get_beast2_example_filename(filename) that returns the full path to a BEAST2 example filename, or calls stop if the file is absent

Get 100% code coverage again under Linux

Check if vignette works

install_beast2 fails on MacOS Sierra: status 403 Forbidden

On MacOS Sierra 10.13.4 I get:

beastier::install_beast2()
downloaded 0 bytes

Error in utils::download.file(url = url, destfile = local_path) :
cannot download all files
In addition: Warning message:
In utils::download.file(url = url, destfile = local_path) :
URL 'https://github-production-release-asset-2e65be.s3.amazonaws.com/15949777/f0f47ba0-fb6e-11e7-98fc-590aa8a9cf5b?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180511%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180511T074241Z&X-Amz-Expires=300&X-Amz-Signature=efaecee27d6347c4fe1aca611dd5387496fe377b2c68f1dea67be5f64221b19f&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DBEAST.v2.4.8.Linux.tgz&response-content-type=application%2Foctet-stream': status was '403 Forbidden'

Can beastier run on Peregrine?

There is evidence not any more

Fix CRAN build

Feedback from Brian Ripley:

See https://cran.r-project.org/web/checks/check_results_beastier.html .

Your test seems wrong-headed: nothing mandates paths should start at /home on Unix: macOS uses /Users, my dept uses /homes for roving home directories and /users is quite common. And installing into ~/.local/share would be a violation of the CRAN policy ....

Please correct ASAP once all the results are in and before Jun 6 to safely retain the package on CRAN.

He is (of course) right!

Let beastier write to a folder in the cache, allow to delete it

An informal feature request by @thijsjanzen.

I think it would be a good idea to:

let beastier write to subfolders of ~/.cache/beastier
add beastier::clear_beastier_cache()

Check if that matters
Give error if it does

Invalid cross-device link

A local-only error:

Error: file.exists(output_log_filename) is not TRUE
In addition: Warning messages:
1: In file.rename(from = from, to = output_log_filename) :
  cannot rename file 'test_output_0.log' to '/tmp/RtmpCkIwGP/file1ef65a706c8.log', reason 'Invalid cross-device link'
2: In file.rename(from = from, to = to) :
 
 Show Traceback
 
 Rerun with Debug
 Error: file.exists(output_log_filename) is not TRUE

Hypothesis: currently, I have two installations of Lubuntu on my HDD. I think the one tmp folder is of the other and older Lubuntu version.

Experiment: re-install Lubuntu on the full HDD and it may be solved.

Can call BEAST2 binary file under Windows

Crashes now under AppVeyor.

run_beast2 should give a warning before overwriting log file

Feedback bjoelle:

run_beast2: I think that this function should give a warning before erasing beast_log_filename and beast_trees_filenames if they exist, because I wouldn't have expected those files to be touched at all if I have specified different values for output_log_filename and output_trees_filenames. A better solution would be to move/rename these files temporarily if they already exist, and restore them once the run is done.

Remove is_beast2_input_file lines handling the BEAST2 exit code

Feedback bjoelle:

is_beast2_input_file: l38-40 should be removed - they don't do anything and status_code is 0 even if the file is invalid

Add 'save_nexus_as_fasta' function

Refactor gives_beast2_warning and is_beast2_input_file

Feedback bjoelle:

gives_beast2_warning: This function has a lot of code in common with is_beast2_input_file, so I would suggest putting the common code in a separate function that would be called by both.

Deprecate BEAST2 options for output filenames

Prevent BEAST2 freeze when overwriting a log file with overwrite set to false

test_that("BEAST2 freezes when treelog file already exists", {

  skip("Issue 50, Issue #50")

  if (!is_beast2_installed()) return()

  beast2_xml_filename <- tempfile(
    pattern = "beast2_", tmpdir = rappdirs::user_cache_dir(),
    fileext = ".xml"
  )

  beautier::create_beast2_input_file_from_model(
    input_filename = beautier::get_fasta_filename(),
    output_filename = beast2_xml_filename,
    inference_model = beautier::create_test_inference_model(
      mcmc = beautier::create_test_mcmc(
        screenlog = beautier::create_screenlog(filename = "")
      )
    )
  )
  testit::assert(file.exists(beast2_xml_filename))

  # First run works fine, takes approx 1 sec on my computer
  beastier::run_beast2_from_options(
    beastier::create_beast2_options(
      input_filename = beast2_xml_filename,
      overwrite = FALSE,
      verbose = TRUE
    )
  )

  # Second run causes BEAST2 to freeze
  beastier::run_beast2_from_options(
    beastier::create_beast2_options(
      input_filename = beast2_xml_filename,
      overwrite = FALSE,
      verbose = TRUE
    )
  )

})

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