The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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BEAST 2.1.3

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"BEAST 2 is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results." (BEAST2 wiki main page)

Bouckaert R, Heled J, Kühnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) "BEAST2: A software platform for Bayesian evolutionary analysis". PLOS Computational Biogogy 10(4): e1003537, 2014. doi:10.1371/journal.pcbi.1003537 full text

BEAST analyses done through the DE are run on the Stampede supercomputer at the Texas Advanced Computing Center, which has queue. If there are many jobs in the backlog, which can happen randomly, but especially after they have had a service outage, there may be a long wait time in the queue. This app is set up to run for the maximum run time (48 hours) so that it can handle fairly large analyses. Because of the long run time, it does not move as quickly through the queue. Therefore, for very small jobs, when you combine the wait time and the processing time, it may not be much faster to run BEAST through the DE than on a desktop computer, but for large jobs, it should be much faster.

Quick Start

  • To use BEAST 2.1.3, upload an XML file generated by BEAUti 2.1.3.
  • See the BEAST help page for more information on using BEAUti.
  • Click on the app "BEAST" under the High-Performance Computing category.
  • Rename your analysis something meaningful. You can add comments and change where the results are stored if you want. BEAST will by default save your input file, so it doesn't matter if you check "save inputs".
  • Click on the input pane and select your XML input file. Note that XML files generated by older versions of BEAUti will not work.
  • If you want to change or add parameters, click on the parameters panel and add each one separated by a space. Be sure to format the parameters as specified for running BEAST on the command line (see Resources, below).
    • This is a High Performance Computing (HPC) application designed to run on a graphical processing unit (GPU) on the Stampede supercomputer at the Texas Advance Computing Center. Because of this, it will generally run the fastest using the default parameter (-beagle_gpu).
  • Click the Launch Analysis button.
  • There is a 24 hour time limit on this application. For large jobs, it is recommended that you first submit and XML file with a small number of generations (e.g., 1 million) to determine how many generations your analysis can get through in 24 hours and then set up your main analysis accordingly. Jobs that do not completely finish should still give output at the end of 24 hours.
  • Remember, because this is an HPC app, the wait time once the job is submitted may be longer than you are used to. On the other hand, once it starts to run, it is really fast!

Resources

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> BEAST2

Input File(s)

Use testGTR.xml from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Output File(s)

  • Expect as output a set of files prefixed with the name of the input file. The exact output files will depend on specifications of the input XML
  • If you use the test file above, your output should be:
    • Job_id.err – standard error
    • Job_id.out – standard output
    • test.random_number.log
    • test.random_number.trees
    • testGTR.xml
    • testGTR.xml.state

Evaluate the output

To view, download the output and open it in Tracer or TreeAnnotator (which come with BEAST2 when you download it). Alternatively, you can use the ??BEAST-2.1.3 Atmosphere image which comes with the full BEAST package installed (including beauti, beast, densitree, logcombiner, and treeannotator). From there, you can use the desktop iDrop app to upload your output files and view and manipulate them, without having to download them to your desktop.

Tool Source for App

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