LogCombiner on XSEDE1.8.4Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDERemco 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 / Alignmentlogcombinerbeast3_trestlesperl$which_beast eq "4"perl""0number_nodes2scheduler.confperl
"nodes=1\\n" .
"node_exclusive=0\\n" .
"threads_per_process=3\\n"
infileInput Fileperl"logfile1.txt"80logfile1.txtall_results*which_beastWe currently only support 1.8.444Please choose a BEAST versionperl!defined $which_beast4We can add more versions, just send a request. We can get it done in a day or so.runtime1scheduler.confMaximum Hours to Run (up to 168 hours)0.5The maximum hours to run must be less than 168perl$runtime > 168.0The maximum hours to run must be greater than 0.05perl$runtime < 0.05perl"runhours=$value\\n"The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hoursperl$runtime > 0Estimate 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_typeWhat file type?lgfilestreesperl($value ne $vdef) ? "-trees":""lgfilesPlease specify your file typeperl!defined $file_type4set_decimalConvert numbers from scientific to decimal notation (-decimal)perl ($value) ? "-decimal" : ""05This option will help the application determine how to run the jobresample_valResample the log files to lower frequency (-resample)perl (defined $value) ? "-resample $value" : ""4This number must be a multiple of original specified sampling frequency. If you sampled every 1000 states, you can use any integer multiple of 1000scale_factorScaling factor for time (-scale)perl (defined $value) ? "-scale $value" : ""4Specify a scaling factor that will multiply any time units by this valueset_burnin5Set the number of states for burn-in (-burnin)perl (defined $value) ? "-burnin $value":""200This option will help the application determine how to run the jobnum_logfilesHow many more log files do you need to upload? (0-5)012345log_file2Choose your second log fileperl$num_logfiles > 0perl "logfile2.txt"Please supply logfile 2perl$num_logfiles > 0 && !defined $log_file2logfile2.txt81log_file3Choose your third log fileperl$num_logfiles > 1perl "logfile3.txt"Please supply logfile 3perl$num_logfiles > 1 && !defined $log_file3logfile3.txt82log_file4Choose your fourth log fileperl$num_logfiles > 2perl "logfile4.txt"Please supply logfile 4perl$num_logfiles > 2 && !defined $log_file4logfile4.txt83log_file5Choose your fifth log fileperl$num_logfiles > 3perl "logfile5.txt"Please supply logfile 5perl$num_logfiles > 3 && !defined $log_file5logfile5.txt84log_file6Choose your sixth log fileperl$num_logfiles > 4perl "logfile6.txt"Please supply logfile 6perl$num_logfiles > 3 && !defined $log_file6logfile6.txt84set_outputSpecify the name of the output fileperl "$value"out.txt99Please specify an output nameperl!$set_outputThis option will help the application determine how to run the job