{"id":6593,"date":"2022-12-08T15:01:16","date_gmt":"2022-12-08T15:01:16","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=6593"},"modified":"2024-07-24T14:46:05","modified_gmt":"2024-07-24T13:46:05","slug":"beast-2","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/a-z\/beast-2\/","title":{"rendered":"BEAST 2"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/www.beast2.org\">Beast2<\/a><\/p>\n<p>BEAST (Bayesian Evolutionary Analysis Sampling Trees) is an application for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 Markov chain Monte Carlo (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.<\/p>\n<p>Versions 2.6.7 and 2.7.0 are installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>BEAST 2 is free software; you can redistribute it and\/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.<br \/>\nBeast2 may be cited using the primary website: Bouckaert R.\u2013 BEAST 2.5 \u2013 <a href=\"https:\/\/www.beast2.org\/citation\/\">https:\/\/www.beast2.org\/citation\/ <\/a><\/p>\n<h2>Set up procedure<\/h2>\n<p>You will be able to access the executables by using one of the following module commands:<\/p>\n<pre>module load apps\/binapps\/beast2\/2.7.0\r\nmodule load apps\/binapps\/beast2\/2.6.7\r\n<\/pre>\n<p>It is recommended loading modulefiles within your jobscript and let the job <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>. Please do not run beast2 on the login node. Jobs should be submitted to the compute nodes via batch or run interactively, following the examples provided below.<\/p>\n<h2>Running the application<\/h2>\n<h3>Example of interactively running BEAST2<\/h3>\n<pre>module load apps\/binapps\/beast2\/2.7.0\r\n\r\n#reserving 2 cores\r\nqrsh -l short -pe smp.pe 2 beast testBSP.xml\r\n\r\n#or requesting for the v100 GPU\r\nqrsh -V -cwd -pe smp.pe 2 -l v100 beast testBSP.xml\r\n\r\n<\/pre>\n<p>Program descriptions and options are shown when running:<\/p>\n<pre>qrsh -l short -pe smp.pe 2\r\nbeast -help<\/pre>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n### You may need to add a high memory flag here e.g.\r\n#$ -l mem512\r\n\r\n# Choose your required version\r\nmodule load apps\/binapps\/beast2\/2.7.0\r\n\r\nbeast testBSP.xml<output>\r\n\r\n<\/output><\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<p>If you need more RAM (memory) to complete the analysis successfully, or you receive a similar error message with,<\/p>\n<pre>Error occurred during initialization of VM\r\nCould not reserve enough space for 8388608KB object heap<\/pre>\n<p>then please add the flags mentioned at the <a href=\"\/csf3\/batch\/high-memory-jobs\/\">high-memory jobs<\/a> page for more information.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 4     # Number of cores, can be 2--32\r\n### You may need to add a high memory flag here e.g.\r\n#$ -l mem512\r\n\r\n# Choose your required version\r\nmodule load apps\/binapps\/beast2\/2.7.0\r\n\r\n# Need to add the \"-thread\" flag and \r\n# $NSLOTS will automatically set to the number of cores requested above\r\nbeast -threads $NSLOTS testBSP.xml<output>\r\n\r\n<\/output><\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<p>If you need more RAM (memory) to complete the analysis successfully, and you may well do!, please add the flags mentioned at the <a href=\"\/csf3\/batch\/high-memory-jobs\/\">high-memory jobs<\/a> page for more information.<\/p>\n<h2>Further information<\/h2>\n<ul>\n<li><a href=\"http:\/\/beast.community\/index.html\">BEAST2 Docs<\/a><\/li>\n<li><a href=\"https:\/\/www.beast2.org\/tutorials\/\">BEAST2 Tutorials<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Beast2 BEAST (Bayesian Evolutionary Analysis Sampling Trees) is an application for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/a-z\/beast-2\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":36,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-6593","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6593","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=6593"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6593\/revisions"}],"predecessor-version":[{"id":7865,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6593\/revisions\/7865"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/36"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=6593"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}