MrBayes Restart on ACCESS 3.2.x Tree Inference Using Bayesian Analysis - run on XSEDE John P. Huelsenbeck and Fred Ronquist Huelsenbeck, J. P. and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755. Ronquist, F. and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. . Phylogeny / Alignment mrbayes_restart_xsede mbmpi_326 perl $run_version == "6" perl "" 0 mbmpi_327 perl $run_version == "7" perl "" 0 mpi_processes_conf1 3 scheduler.conf perl !$more_memory perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "threads_per_process=1\\n" . "node_exclusive=0\\n" . "mpi_processes=" . $nchains_specified * $nruns_specified . "\\n" mpi_processes_conf1b 3 scheduler.conf perl $more_memory perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem_expanse=" . (int($nchains_specified * $nruns_specified*8)) . "G\\n" . "threads_per_process=1\\n" . "threads_per_process_expanse=4\\n" . "node_exclusive=0\\n" . "mpi_processes=" . $nchains_specified * $nruns_specified . "\\n" infile Input File (must be in Nexus format) (-execute) paramfile.txt perl "execute infile.nex\\n" 2 infile.nex ALL_FILES * run_version I am restarting a checkpoint from 6 7 7 nruns_specified 1 My MrBayes Block specifies nruns= scheduler.conf 2 The values entered for nruns and nchains influence the number of cpu's that can be used in parallel. Please enter the value you specified for nruns in the MrBayes block of the Nexus file. If you didn't specify a value for nruns, please leave this field at its default value of 2. Please enter a value for nruns perl !$nruns_specified The value of nruns must be greater than 0 perl $nruns_specified < 1 nchains_specified 1 My MrBayes Block specifies nchains= scheduler.conf 4 The value entered for nruns and nchains influences the number of cpu's that can be used in parallel. Enter the value you specified for nchains in the MrBayes block of the nexus file. If you didn't specify a value for nchains, please leave this field at its default value of 4. Please enter value for nchains perl !$nchains_specified The value of nchains must be greater than 0 perl $nchains_specified < 1 nruns x nchains must be less than or equal to 24. perl ($nruns_specified * $nchains_specified > 24) nruns x nchains must be a multiple of 2 perl ((($nruns_specified * $nchains_specified) % 2) != 0) runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 Please enter a positive number for the maximum runtime perl $runtime < 0 Please specify a maximum runtime perl !defined $runtime perl "runhours=$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 $nchains_specified * $nruns_specified == 2 The job will run on 4 processors as configured. If it runs for the entire configured time, it will consume 4 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 4 The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 6 The job will run on 8 processors as configured. If it runs for the entire configured time, it will consume 8 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 8 The job will run on 10 processors as configured. If it runs for the entire configured time, it will consume 10 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 10 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 12 The job will run on 14 processors as configured. If it runs for the entire configured time, it will consume 14 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 14 The job will run on 16 processors as configured. If it runs for the entire configured time, it will consume 16 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 16 The job will run on 40 processors as configured. If it runs for the entire configured time, it will consume 40 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 10 Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. more_memory I need more memory 1 Choosing this option will increase your memory by 4 fold, and increase the charge by 4 fold as well. set_beagle_params Run BEAGLE paramfile.txt 1 Disabling BEAGLE will slow your run by as much as 20%. You should only do this if a run with BEAGLE fails, or if you believe using BEAGLE gave you unexpected results. perl !$set_beagle_params We have seen examples where MrBayes runs on BEAGLE can produce anomalous topolgies. If you see an odd topology, please try the run without BEAGLE perl $set_beagle_params Beagle should speed up runs by about 10-20%. You should only disble this parameter if you have a problem using Beagle. set_beagle_params6 paramfile.txt perl $set_beagle_params && $run_version > "5" perl "set usebeagle=yes beagleprecision=double beaglesse=yes beaglescaling=dynamic beaglethreads=no\\n" set_beagle_params7 paramfile.txt perl !$set_beagle_params && $run_version > "5" perl "set usebeagle=no\\n" upload_ckpfile 2 Choose the Checkpoint File (.ckp) infile.nex.ckp upload_mcmcfile 2 Choose the mcmc File (.mcmc) infile.nex.mcmc Please select the mcmc file to upload perl !defined $upload_mcmcfile upload_ssfile 2 Choose the Stepping Stone File (.ss) infile.nex.ss num_tfiles 2 How many Sumt files do you wish to use? 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 upload_sumtfile1 2 Select Sumt File 1 (.t) infile.nex.run1.t perl $num_tfiles > 1 Please select the first Sumt file to upload perl !defined $upload_sumtfile1 && $num_tfiles > 1 upload_sumtfile1b 2 Select Sumt File 1 (.t) infile.nex.t perl $num_tfiles == 1 Please select the first Sumt file to upload perl !defined $upload_sumtfile1b && $num_tfiles == 1 upload_sumtfile2 2 Select Sumt File 2 (.t) perl $num_tfiles > 1 infile.nex.run2.t Please select the second Sumt file to upload perl !defined $upload_sumtfile2 upload_sumtfile3 2 Select Sumt File 3 (.t) perl $num_tfiles > 2 infile.nex.run3.t Please select the third Sumt file to upload perl !defined $upload_sumtfile3 upload_sumtfile4 2 Select Sumt File 4 (.t) perl $num_tfiles > 3 infile.nex.run4.t Please select the fourth Sumt file to upload perl !defined $upload_sumtfile4 upload_sumtfile5 2 Select Sumt File 5 (.t) infile.nex.run5.t perl $num_tfiles > 4 Please select the fifth Sumt file to upload perl !defined $upload_sumtfile5 upload_sumtfile6 2 Select Sumt File 6 (.t) perl $num_tfiles > 5 infile.nex.run6.t Please select the sixth Sumt file to upload perl !defined $upload_sumtfile6 upload_sumtfile7 2 Select Sumt File 7 (.t) perl $num_tfiles > 6 infile.nex.run7.t Please select the seventh Sumt file to upload perl !defined $upload_sumtfile7 upload_sumtfile8 2 Select Sumt File 8 (.t) perl $num_tfiles > 7 infile.nex.run8.t Please select the eigth Sumt file to upload perl !defined $upload_sumtfile8 upload_sumtfile9 2 Select Sumt File 9 (.t) perl $num_tfiles > 8 infile.nex.run9.t Please select the ninth Sumt file to upload perl !defined $upload_sumtfile9 upload_sumtfile10 2 Select Sumt File 10 (.t) perl $num_tfiles > 9 infile.nex.run10.t Please select the tenth Sumt file to upload perl !defined $upload_sumtfile10 upload_sumtfile11 2 Select Sumt File 11 (.t) perl $num_tfiles > 10 infile.nex.run11.t Please select the eleventh Sumt file to upload perl !defined $upload_sumtfile11 upload_sumtfile12 2 Select Sumt File 12 (.t) perl $num_tfiles > 11 infile.nex.run12.t Please select the twelfth Sumt file to upload perl !defined $upload_sumtfile12 upload_sumtfile13 2 Select Sumt File 13 (.t) infile.nex.run13.t perl $num_tfiles > 12 Please select the thirteenth Sumt file to upload perl !defined $upload_sumtfile13 upload_sumtfile14 2 Select Sumt File 14 (.t) perl $num_tfiles > 13 infile.nex.run14.t Please select the fourteenth Sumt file to upload perl !defined $upload_sumtfile14 upload_sumtfile15 2 Select Sumt File 15 (.t) perl $num_tfiles > 14 infile.nex.run15.t Please select the fifteenth Sumt file to upload perl !defined $upload_sumtfile15 upload_sumtfile16 2 Select Sumt File 16 (.t) perl $num_tfiles > 15 infile.nex.run16.t Please select the sixteenth Sumt file to upload perl !defined $upload_sumtfile16 upload_sumtfile17 2 Select Sumt File 17 (.t) perl $num_tfiles > 16 infile.nex.run17.t Please select the seventeenth Sumt file to upload perl !defined $upload_sumtfile17 upload_sumtfile18 2 Select Sumt File 18 (.t) perl $num_tfiles > 17 infile.nex.run18.t Please select the eighteenth Sumt file to upload perl !defined $upload_sumtfile18 upload_sumtfile19 2 Select Sumt File 19 (.t) perl $num_tfiles > 18 infile.nex.run19.t Please select the nineteenth Sumt file to upload perl !defined $upload_sumtfile19 upload_sumtfile20 2 Select Sumt File 20 (.t) perl $num_tfiles > 19 infile.nex.run20.t Please select the twentieth Sumt file to upload perl !defined $upload_sumtfile20 num_pfiles 2 How many Sump files do you wish to use? 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 upload_sumpfile1 2 Select Sump File 1 (.p) infile.nex.run1.p perl $num_pfiles > 1 Please select the first Sump file for the run perl !defined $upload_sumpfile1 && $num_pfiles > 1 upload_sumpfile1b 2 Select Sump File 1 (.p) infile.nex.p perl $num_pfiles == 1 Please select the Sump file for a single run (nruns=1) perl !defined $upload_sumpfile1b && $num_pfiles == 1 upload_sumpfile2 2 Select Sump File 2 (.p) perl $num_pfiles > 1 infile.nex.run2.p Please select the second Sump file to upload perl !defined $upload_sumpfile2 upload_sumpfile3 2 Select Sump File 3 (.p) perl $num_pfiles > 2 infile.nex.run3.p Please select the third Sump file to upload perl !defined $upload_sumpfile3 upload_sumpfile4 2 Select Sump File 4 (.p) perl $num_pfiles > 3 infile.nex.run4.p Please select the fourth Sump file to upload perl !defined $upload_sumpfile4 upload_sumpfile5 2 Select Sump File 5 (.p) perl $num_pfiles > 4 infile.nex.run5.p Please select the fifth Sump file for the run perl !defined $upload_sumpfile5 upload_sumpfile6 2 Select Sump File 6 (.p) perl $num_pfiles > 5 infile.nex.run6.p Please select the sixth Sump file to upload perl !defined $upload_sumpfile6 upload_sumpfile7 2 Select Sump File 7 (.p) perl $num_pfiles > 6 infile.nex.run7.p Please select the seventh Sump file to upload perl !defined $upload_sumpfile7 upload_sumpfile8 2 Select Sump File 8 (.p) perl $num_pfiles > 7 infile.nex.run8.p Please select the eigth Sump file to upload perl !defined $upload_sumpfile8 upload_sumpfile9 2 Select Sump File 9 (.p) perl $num_pfiles > 8 infile.nex.run9.p Please select the ninth Sump file for the run perl !defined $upload_sumpfile9 upload_sumpfile10 2 Select Sump File 10 (.p) perl $num_pfiles > 9 infile.nex.run9.p Please select the tenth Sump file to upload perl !defined $upload_sumpfile10 upload_sumpfile11 2 Select Sump File 11 (.p) perl $num_pfiles > 10 infile.nex.run11.p Please select the eleventh Sump file to upload perl !defined $upload_sumpfile11 upload_sumpfile12 2 Select Sump File 12 (.p) perl $num_pfiles > 11 infile.nex.run12.p Please select the twelfth Sump file to upload perl !defined $upload_sumpfile12 upload_sumpfile13 2 Select Sump File 13 (.p) perl $num_pfiles > 12 infile.nex.run13.p Please select the thirteenth Sump file for the run perl !defined $upload_sumpfile13 upload_sumpfile14 2 Select Sump File 14 (.p) perl $num_pfiles > 13 infile.nex.run14.p Please select the fourteenth Sump file to upload perl !defined $upload_sumpfile14 upload_sumpfile15 2 Select Sump File 15 (.p) perl $num_pfiles > 14 infile.nex.run15.p Please select the fifteenth Sump file to upload perl !defined $upload_sumpfile15 upload_sumpfile16 2 Select Sump File 16 (.p) perl $num_pfiles > 15 infile.nex.run16.p Please select the sixteenth Sump file to upload perl !defined $upload_sumpfile16 upload_sumpfile17 2 Select Sump File 17 (.p) perl $num_pfiles > 16 infile.nex.run17.p Please select the seventeenth Sump file for the run perl !defined $upload_sumpfile17 upload_sumpfile18 2 Select Sump File 18 (.p) perl $num_pfiles > 17 infile.nex.run18.p Please select the eighteenth Sump file to upload perl !defined $upload_sumpfile18 upload_sumpfile19 2 Select Sump File 19 (.p) perl $num_pfiles > 18 infile.nex.run19.p Please select the nineteenth Sump file to upload perl !defined $upload_sumpfile19 upload_sumpfile20 2 Select Sump File 20 (.p) perl $num_pfiles > 19 infile.nex.run20.p Please select the twentieth Sump file to upload perl !defined $upload_sumpfile20