LogCombiner on XSEDE 1.8.4-2.6.0 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 logcombiner beast4_comet perl $which_beast eq "4" perl "" 0 beast104_comet perl $which_beast eq "104" perl "" 0 beast260_comet perl $which_beast eq "260" perl "" 0 number_nodes 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=3\\n" infile Input File 80 logfile1.txt infile_beast perl $which_beast < 200 perl "logfile1.txt" 80 infile_beast2 perl $which_beast > 200 perl "-log logfile1.txt" 80 all_results * which_beast Choose your Beast/Beast2 Version 4 104 260 104 Please choose a BEAST version perl !defined $which_beast 4 We can add more versions, just send a request. We can get it done in a day or so. 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 1 processor as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hours perl $runtime > 0 Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. file_type What file type? lgfiles trees perl ($value ne $vdef) ? "-trees":"" lgfiles Please specify your file type perl !defined $file_type 4 set_decimal Convert numbers from scientific to decimal notation (-decimal) perl ($value) ? "-decimal" : "" 0 5 This option will help the application determine how to run the job resample_val Resample the log files to lower frequency (-resample) perl (defined $value) ? "-resample $value" : "" 4 This number must be a multiple of original specified sampling frequency. If you sampled every 1000 states, you can use any integer multiple of 1000 scale_factor Scaling factor for time (-scale) perl $which_beast < 200 perl (defined $value) ? "-scale $value" : "" 4 Specify a scaling factor that will multiply any time units by this value set_burnin1 5 Set the number of states for burn-in (-burnin; Beast) perl $which_beast < 200 perl (defined $value) ? "-burnin $value":"" 200 Please enter a burnin value perl !defined $set_burnin1 set_burnin2 5 Set the Percentage of states for burn-in (-b; Beast2) perl $which_beast > 200 perl ($value) ? "-b $value":"" 10 Please enter a burnin value between 1 and 100 perl !defined $set_burnin2 Please enter a burnin value between 1 and 100 perl $set_burnin2 > 100 Please enter a burnin value between 1 and 100 perl $set_burnin2 < 1 This option will help the application determine how to run the job num_logfiles How many more log files do you need to upload? (0-5) 0 1 2 3 4 5 log_file2 Choose your second log file perl $num_logfiles > 0 Please supply logfile 2 perl $num_logfiles > 0 && !defined $log_file2 logfile2.txt 81 infile_beast_a perl defined $log_file2 && $which_beast < 200 perl "logfile2.txt" 81 infile_beast2_a perl defined $log_file2 && $which_beast > 200 perl "-log logfile2.txt" 81 log_file3 Choose your third log file perl $num_logfiles > 1 Please supply logfile 3 perl $num_logfiles > 1 && !defined $log_file3 logfile3.txt 82 infile_beast_b perl defined $log_file3 && $which_beast < 200 perl "logfile3.txt" 82 infile_beast2_b perl defined $log_file3 && $which_beast > 200 perl "-log logfile3.txt" 82 log_file4 Choose your fourth log file perl $num_logfiles > 2 Please supply logfile 4 perl $num_logfiles > 2 && !defined $log_file4 logfile4.txt 83 infile_beast_c perl defined $log_file4 && $which_beast < 200 perl "logfile4.txt" 84 infile_beast2_c perl defined $log_file4 && $which_beast > 200 perl "-log logfile4.txt" 84 log_file5 Choose your fifth log file perl $num_logfiles > 3 Please supply logfile 5 perl $num_logfiles > 3 && !defined $log_file5 logfile5.txt 84 infile_beast_d perl defined $log_file5 && $which_beast < 200 perl "logfile5.txt" 85 infile_beast2_d perl defined $log_file5 && $which_beast > 200 perl "-log logfile5.txt" 85 log_file6 Choose your sixth log file perl $num_logfiles > 4 Please supply logfile 6 perl $num_logfiles > 3 && !defined $log_file6 logfile6.txt 84 infile_beast_f perl defined $log_file6 && $which_beast < 200 perl "logfile6.txt" 86 infile_beast2_f perl defined $log_file6 && $which_beast > 200 perl "-log logfile6.txt" 86 set_output Specify the name of the output file out.txt 99 Please specify an output name perl !$set_output outfile_beast_a perl $which_beast < 200 perl "$set_output" 99 outfile_beast2_a perl $which_beast > 200 perl "-o $set_output" 99