TreeAnnotator on XSEDE 1.8.4-2.6.6 Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE Remco Boukaert, Alexei Drummond, Andrew Rambaut, and Marc A. Suchard Drummond, A. J. and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214. Suchard, M.A. and A. Rambaut. 2009. Many-Core algorithms for statistical phylogenetics. Bioinformatics XX:1-9. Phylogeny / Alignment treeannotator beast4_comet perl $which_beast eq "4" perl "" 0 beast104_comet perl $which_beast eq "104" perl "" 0 beast266_expanse perl $which_beast > "200" perl "" 0 number_nodes 2 scheduler.conf perl $which_beast < 200 && !$more_memory perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=16G\\n" . "threads_per_process=4\\n" number_nodesb 2 scheduler.conf perl $which_beast < 200 && $more_memory perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=64G\\n" . "threads_per_process=4\\n" number_nodes2 2 scheduler.conf perl $which_beast > 200 && !$more_memory perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=16G\\n" . "threads_per_process=4\\n" number_nodes2b 2 scheduler.conf perl $which_beast > 200 && $more_memory perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=64G\\n" . "threads_per_process=4\\n" infile Input File (must be a tree file) perl "infile.trees" 98 infile.trees all_results * which_beast Choose your beast/beast2 version 4 104 266 104 Please choose a BEAST version perl !defined $which_beast 4 This option is offered because sometimes a bug in the interface between BEAST and BEAGLE prevents a run from completing. Use this option if you wish to run a data set that has failed using the normal BEAST/BEAGLE implementation. Runs made this way are always slower, so use this option as a last resort. runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 perl "runhours=$value\\n" The job will run on 2 processors as configured. If it runs for the entire configured time, it will consume 2 X $runtime cpu hours perl $runtime > 0 Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. more_memory I need more memory burnin_type Specify the burnin as perl $which_beast < 200 perl states trees states 4 set_burnin 5 Burnin (as states) (-burnin) perl $burnin_type eq "states" && $which_beast < 200 perl "-burnin $value" 200 Please enter an integer for burnin states perl !defined $set_burnin set_burnintrees 5 Burnin (as trees) (-burnintrees) perl $burnin_type eq "trees" && $which_beast < 200 perl "-burnintrees $value" 200 Please enter an integer for burnin trees perl !defined $set_burnintrees set_burnin2 5 Burnin as percentage of states (-b) perl $which_beast > 200 perl "-b $value" Please enter an integer for percentage of burnin states perl !defined $set_burnin2 Please enter an integer for burnin between 1 and 100 perl $set_burnin2 > 100 Please enter an integer for burnin between 1 and 100 perl $set_burnin2 < 1 use_lowmem 5 Use the low memory option (-lowMem) perl $which_beast > 200 perl "-lowMem" set_limit Posterior probability limit (-limit) perl (defined $value) ? "-limit $value":"" Sorry, the value for minimum posterior probability must be less than 1 perl $set_limit > 1 6 This option will help the application determine how to run the job tree_type Target tree type (-heights) MCC UTT keep 4 tree_heights Set the tree heights (-heights) perl "-heights $value" keep median mean ca keep 4 tree_file Specify a target tree file perl $tree_type eq "UTT" perl "-target target.trees" Please supply a target tree perl $tree_type eq "UTT" && !$tree_file target.trees 7 force_discrete Force integer traits to be treated as discrete traits (-forceDiscrete) perl ($value) ? "-forceDiscrete":"" 0 10 This option will help the application determine how to run the job hpd_interval HPD interval to be used for the bivariate traits (-hpd2D) perl (defined $hpd_interval) ? "-hpd2D $value" : "" 0.95 10 Please specify an HPD interval less than 1 perl $hpd_interval > 1 If this value is left blank, the default (0.80) will apply. no_hpd2D Suppress calculation of HPD intervals for the bivariate traits (-nohpd2D) perl $which_beast > 200 perl ($value) ? "-nohpd2D" : "" 10 not_ancestral Interpret tree set as not being from a sampled ancestor analysis (-noSA) perl $which_beast > 200 perl ($value) ? "-noSA" : "" 10 set_output Specify the name of the output file perl "$value" out.txt 99 Please specify an output name perl !$set_output This option will help the application determine how to run the job