1.0 IMa2p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model Arun Sethuraman and Jody Hey Arun Sethuraman and Jody Hey (2016) IMa2p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model Mol Ecol Resour. 2016 Jan; 16(1): 206–215. Hey J. 2010. Isolation with Migration Models for More Than Two Populations. Mol Biol Evol 27: 905-20 Phylogeny / Alignment ima2_xsede ima2p_invoke2 perl "ima2p_1.0_comet" 0 command_line 0 perl "" number_nodes1 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\\n" . "jobtype=mpi\\n" . "mpi_processes=1\\n" infile Input infile.txt perl "-i infile.txt" 1 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 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $specify_runtype == 1 The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hours perl $specify_runtype == 2 && $specify_numparts > 12 The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hours perl $specify_runtype == 2 && $specify_numparts == 1 && $specify_mem > 60 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 $specify_runtype == 2 && $specify_numparts < 13 && !defined $specify_mem 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 $specify_runtype == 2 && $specify_numparts == 1 && defined $specify_mem && $specify_mem < 60 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. choose_runmethod Run duration (-l) in: perl $specify_runtype ne 0 || !defined $specify_runtype 1 Number of genealogies to save 2 Time in hours between outputs Please choose the run duration method perl !defined $choose_runmethod specify_genealogies Specify the number of genealogies to save (-l integer) perl $choose_runmethod == 1 perl (defined $value) ? "-l $value":"" specify_readgenealogies Specify the number of genealogies to read from file (-l integer) perl $specify_runtype == 0 perl (defined $value) ? "-l $value":"" specify_hours Hours between writing of burntrend file (-l) perl $specify_runtype ne 0 && $choose_runmethod == 2 perl (defined $value) ? "-l $value":"" migration_prior Migration prior value (-m, maximum for uniform, mean if exponential distribution is used) perl (defined $value) ? "-m $value":"" outfile_name Output file name perl (defined $value) ? "-o $value":"" max_popsize Maximum for population size parameters (-q, 4Nu) perl (defined $value) ? "-q $value":"" specify_seed Random number seed (-s default is taken from current time) perl (defined $value) ? "-s $value":"" specify_popsplit Maximum time of population splitting (-t) perl (defined $value) ? "-t $value":"" specify_tiname Base name (no extension) of *.ti files with genealogy data perl $specify_runtype == 0 perl (defined $value) ? "-v $value":"" specify_mutratescalar Mutation rate scalar for relevant loci -for use with -p3 (-y) perl $specify_output == 3 perl (defined $value) ? "-y $value":"" specify_stepscreen Base name (no extension) of *.ti files with genealogy data perl $specify_runtype == 0 perl (defined $value) ? "-v $value":"" specify_runtype Specify the run type (-r) 0 Load genealogies from previous run(s) 1 Do not save genealogies to a file 2 Save the state of the Markov chain in a file 3 Start run by loading a previously saved *.mcf file 4 Write all mutation related updates rates to stdout 5 Print burntrend file at end of burnin period perl (!defined $value) ? "-r $value":"" specify_calcoption Specify the calculation option (-c) 0 Likelihood of data functions return a constant 1 Include ranges on mutation rates as priors 2 Joint posterior density calculations 3 Get prior distribution terms from file perl (defined $value) ? "-c $value":"" For the calculation options (-c): 0 Likelihood of data functions return a constant -posterior should equal prior 1 Include ranges on mutation rates as priors on mutation rate scalars 2 Joint posterior density calculations, for LLR tests of nested models use with -w (LOAD- GENEALOGY mode only) 3 Get prior distribution terms from file (requires filename given with -g) choose_burninsteps Burn duration (-b) is in: perl $specify_runtype ne 0 || !defined $specify_runtype 1 Number of Burnin Steps 2 Time in hours between writing to burntrend Please choose the burnin method perl !defined $choose_burninsteps specify_burninsteps Specify the number of burnin steps (-b integer) perl $choose_burninsteps == 1 perl (defined $value) ? "-b $value":"" specify_burntrend Hours between writing of burntrend file (-b float; there must be a decimal) perl $specify_runtype ne 0 && $choose_burninsteps == 2 perl (defined $value) ? "-b $value":"" heating_terms Heating Terms specify_heatingmodel Specify the heating model (-hf) perl $specify_runtype ne 0 || !defined $specify_runtype g geometric l linear l perl "-hf$value" Please select a heating model perl !defined $specify_heatingmodel specify_numchains Number of chains (-hn) perl defined $value ? "-hn$value":"" specify_swapchains Number of swap chains (-hk) perl $specify_runtype ne 0 || !defined $specify_runtype perl defined $value ? "-hk$value":"" specify_firstheatparam Specify the first heating parameter (-ha) perl $specify_runtype ne 0 || !defined $specify_runtype perl defined $value ? "-ha$value":"" specify_secondheatparam Specify the second heating parameter (-hb) perl $specify_runtype ne 0 || !defined $specify_runtype perl defined $value ? "-hb$value":"" specify_numsteps Specify the number of steps between geneology saving (-d) perl $specify_runtype ne 0 || !defined $specify_runtype perl defined $value ? "-d $value":"" 100 specify_modeloptions Specify the model (-j) 1 Migration only between sister populations 2 One migration parameter for each pair of populations 3 Migration only between sampled populations 4 Add a non-sampled ghost population to the model 5 Separate population size and migration parameters in each period 6 No migration in the model 7 Migration prior follows exponential distribution with mean given by -m or in parameter prior file 8 Each ancestral population size is assumed to identical to that of their largest descendant population 9 One single migration parameter for all pairs of populations perl (defined $value) ? "-j $value":"" specify_output Specify the output type (-p) perl "-p $value" 0 Turn off trend plots in outfile (default is to print trend plots) 1 Turn off plots of marginal curves in outfile (default is to print marginal density plots) 2 Print TMRCA histogram for each genealogy (MCMC mode only) 3 Print histogram of parameters on demographic scales (requires mutation rate(s) in data file) 4 Print histogram of splitting times divided by prior (do not use with -j0 or when only 2 sampled populations 5 Print estimates and histograms of population migration rate (2NM) 6 Print pairwise probabilities that one parameter is greater than another 7 Print histograms of the number of migration events (MCMC mode only) 8 Print joint estimate for splitting times (MCMC mode only, for models with 3, 4 or 5 populations) specify_gentime Generation time in years - for use with -p3 (default is 1) perl $specify_output == 3 perl (defined $value) ? "-u $value":"" 1 markovchainstate_file Select the .mcf file with saved Markov chain state generated in previous run perl $specify_runtype eq 3 markovchainstate.mcf perl defined $value ? "-f markovchainstate.mcf":"" results *