1.13 IMa3p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model Jody Hey, Rasmus Nielsen, Sang Chul Choi, Vitor Sousa, Janeen Pisciotta, Yujin Chung and Arun Sethuraman 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., Chung, Y., Sethuraman, A., Lachance, J., Tishkoff, S., Sousa, V. C., and Wang, Y. (2018) Phylogeny Estimation by Integration over Isolation with Migration Models. Molecular Biology and Evolution 35, 2805-2818 Phylogeny / Alignment ima3_xsede ima2p_invoke2 perl "ima3_1.13_expanse" 0 number_nodes1 2 scheduler.conf perl $specify_numchains < 256 perl "nodes=1\\n" . "node_exclusive=0\\n" . "cpus-per-task=1\\n" . "mem=" . (int(($specify_numchains * 0.5)*(248/128))) . "G\\n" . "jobtype=mpi\\n" . "mpi_processes=" . $specify_numchains * 0.5 . "\\n" number_nodes2 2 scheduler.conf perl $specify_numchains >= 256 perl "nodes=1\\n" . "node_exclusive=1\\n" . "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=243G\\n" . "mpi_processes=128\\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 $specify_numchains * 0.5 processors as configured. If it runs for the entire configured time, it will consume $specify_numchains * 0.5 x $runtime cpu hours perl $specify_numchains < 256 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $specify_numchains >= 256 WARNING: This job will consume 3,000-6,000 CPU hours if it runs for the entire configured time. Are you sure you want to do this? perl $specify_numchains >= 256 && $runtime >= 24 && $runtime < 48 WARNING: This job will consume 6,000-9,000 CPU hours if it runs for the entire configured time. Are you sure you want to do this? perl $specify_numchains >= 256 && $runtime >= 48 && $runtime < 72 WARNING: This job will consume 9,000-12,000 CPU hours if it runs for the entire configured time. Are you sure you want to do this? perl $specify_numchains >= 256 && $runtime >= 72 && $runtime < 96 WARNING: This job will consume 12,000-15,000 CPU hours if it runs for the entire configured time. Are you sure you want to do this? perl $specify_numchains >= 256 && $runtime >= 96 && $runtime < 120 WARNING: This job will consume 15,000-18,000 CPU hours if it runs for the entire configured time. Are you sure you want to do this? perl $specify_numchains >= 256 && $runtime >= 120 && $runtime < 144 WARNING: This job will consume 18,000-21,000 CPU hours if it runs for the entire configured time. Are you sure you want to do this? perl $specify_numchains >= 256 && $runtime >= 144 && $runtime <= 168 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. max_popsize Maximum for population size parameters (-q, 4Nu) perl (defined $value) ? "-q $value":"" 50 A value may be required for Maximum for population size perl !defined $max_popsize migration_prior Migration prior value (-m, maximum for uniform, mean if exponential distribution is used) perl (defined $value) ? "-m $value":"" A value may be required for Migration prior value (-m) perl !defined $specify_popsplit 70 Please see the manual for further information about the -m option. outfile_name Output file name perl (defined $value) ? "-o $value":"" 5 specify_seed Random number seed (-s default is taken from current time) perl (defined $value) ? "-s $value":"" 50 specify_popsplit Maximum time of population splitting (-t) perl (defined $value) ? "-t $value":"" 51 run_options Run Options run_option0 Load genealogies from previous run(s) (-r0) perl ($value)? "-r0":"" 30 specify_tiname Base name (no extension) of *.ti files with genealogy data perl $run_option0 perl "-v genealogies" 32 specify_tifile1 Select your *.ti file perl $run_option0 genealogies1.out.ti specify_tifile2 Select your second *.ti file perl $run_option0 && defined $specify_tifile1 genealogies2.out.ti specify_tifile3 Select your third *.ti file perl $run_option0 && defined $specify_tifile2 genealogies3.out.ti run_option1 Do not save genealogies to a file (-r1) perl !$run_option0 perl ($value)? "-r1":"" run_option2 Save the state of the Markov chain in a file (-r2) perl ($value)? "-r2":"" run_option3 Start run by loading a previously saved *.mcf file (-r3) perl ($value)? "-r3":"" markovchainstate_filename Enter the mcf file name (-f) perl $run_option3 perl "-f statefile.mcf" To use this option, -r3 must be invoked. specify_mcffile Specify the first *.mcf file perl $run_option3 statefile.mcf.0 specify_mcffile2 Specify the second *.mcf file perl defined $specify_mcffile statefile.mcf.1 specify_mcffile3 Specify the third *.mcf file perl defined $specify_mcffile2 statefile.mcf.2 specify_mcffile4 Specify the fourth *.mcf file perl defined $specify_mcffile3 statefile.mcf.3 run_option4 Write all mutation related rates to stdout.txt (-r4) perl ($value)? "-r4":"" run_option5 Print burntrend file at end of burnin period (-r5) perl !$run_option0 perl ($value)? "-r5":"" run_option6 When loading mcf files (-r3,-r7), use previous run as burnin (-r6) perl ($value)? "-r6":"" run_option7 Load mcf if present, AND save to mcf (-r7) perl ($value)? "-r7":"" run_option8 Use unique IMburn/run files with outfilename as a prefix (-r8) perl ($value)? "-r8":"" specify_numsteps Specify the number of steps between geneology saving (-d) perl !$run_option0 perl defined $value ? "-d $value":"" 100 The -d option is ignored when sampling phylogenies calculation_options Calculation Options calc_option0 Likelihood of data functions return a constant -posterior should equal prior (-c0) perl ($value)? "-c0":"" calc_option1 Include ranges on mutation rates as priors on mutation rate scalars (-c1) perl ($value)? "-c1":"" calc_option2 Joint posterior density calculations, for LLR tests of nested models (-c2) perl $run_option0 perl ($value)? "-c2":"" 34 specify_nestmod File with nested models to be tested (LOAD-GENEALOGY mode only), invokes -c2 (-w) perl $calc_option2 nested_models.txt perl (defined $value) ? "-w nested_models.txt":"" 36 The -c2 option requres a file with nested models via -w perl $calc_option2 && !defined $specify_nestmod calc_option3 Get prior distribution terms from file (-c3) perl ($value)? "-c3":"" datatype5_file Select file with parameter priors perl $calc_option3 perl (defined $value)? "-g imapriors.txt":"" imapriors.txt Sorry, you cant specify a parameter prior file AND specify a prior via -m perl defined $migration_prior && defined $datatype5_file To use this option, calculation option 3, -c3 must be invoked set_burnin Set Burnin choose_burninsteps Burn duration (-b) is in: perl !$run_option0 && !$run_option7 1 Number of Burnin Steps 2 Time in hours between writing to burntrend Please choose the burnin method perl !defined $choose_burninsteps The -b value is ignored when R7 is used. specify_burninsteps Specify the number of burnin steps (-b integer) perl $choose_burninsteps == 1 perl (defined $value) ? "-b $value":"" specify_burntrend Hours between writing of burntrend file (there must be a decimal) perl !$run_option0 && $choose_burninsteps == 2 perl (defined $value) ? "-b $value":"" heating_terms Heating Terms specify_numchains Number of chains, all models (-hn) perl defined $value ? "-hn$value":"" 20 Please specify the number of chains perl !defined $specify_numchains The number of chains must be a multiple of 2 perl ((($specify_numchains) % 2) != 0) The number of chains must be no greater than 256 perl $specify_numchains > 256 The number of chains must be no less than 4 perl $specify_numchains < 4 specify_firstheatparam Specify the first heating parameter (-ha; sigmoid or geometric) perl defined $value ? "-ha$value":"" 40 This value should be between 0 and 1. Values near 1 will be near Even, values near 0.95 will be sigmoid, specify_secondheatparam Specify the second heating parameter (-hb; geometric only) perl defined $value ? "-hb$value":"" 41 This option is required for the Geometric model model_options Model Options model_option0 Estimate population topology: 3 populations required (-j0) perl ($value)? "-j0":"" specify_topologypr Specify population topology prior (-x) perl $model_option0 perl (defined $value) ? "-x $value":"" Set phylogeny priors for clades of sampled populations (requires -j0), can have multiple -x terms each -x terms must be followed by two or more population integers and a positive floating point value e.g. -x 0 1 2 0.5 sets relative prior on trees with clade consisting of 0,1,2 to 0.5 (default is 1) model_option1 Add a non-sampled ghost population to the model (-j1) perl !$model_option0 perl ($value)? "-j1":"" model_option2 Migration prior follows exponential distribution (-j2) perl ($value)? "-j2":"" model_option3 Use hyperpriors specified by -q and -m (-j3) perl ($value)? "-j3":"" model_option4 Migration only between sister populations (-j4) perl !$model_option0 perl ($value)? "-j4":"" model_option5 One migration parameter for each pair of populations (-j5) perl !$model_option0 perl ($value)? "-j5":"" model_option6 Migration only between sampled populations (-j6) perl !$model_option0 perl ($value)? "-j6":"" model_option7 Period specific parameters (-j7) perl !$model_option0 perl ($value)? "-j7":"" model_option8 No migration in the model (-j8) perl !$model_option0 perl ($value)? "-j8":"" model_option9 One single migration parameter for all pairs of populations (-j9) perl !$model_option0 perl ($value)? "-j9":"" model_optionx One single population size parameter for all populations (-jx) perl !$model_option0 perl ($value)? "-jx":"" Sorry you cant use this option together with Population topology updating and estimation perl $model_option0 && $model_optionx set_runduration Set Run Duration specify_hours Time in hours of the sampling period (must have a decimal) (-L) perl !$run_option0 && $choose_runmethod == 2 perl (defined $value) ? "-L $value":"" Must have a decimal. specify_runduration1 Number of phylogenies to save: perl $model_option0 perl defined $value ? "-L $value":"" Please choose the number of phylogenies to save perl $model_option0 && !defined $specify_runduration1 specify_runduration2b Number of times the genealogies are sampled perl !$model_option0 && !$run_option0 perl defined $value ? "-L $value":"" Please choose the number of genealogies to save perl !$model_option0 && !$run_option0 && !defined $specify_runduration2b The (number of geneologies to save) x (-d) value sets the # of steps in the chain after burnin specify_runduration3 Number of genealogies to load from file perl $run_option0 perl defined $value ? "-L $value":"" 30 Please choose the number of genealogies to load from file perl $run_option0 && !defined $specify_runduration3 The (number of geneologies to save) x (-d) value sets the # of steps in the chain after burnin output_options Output Options output_option0 Turn off trend plots in outfile (-p0) perl ($value)? "-p0":"" 60 output_option1 Turn off plots of marginal curves in outfile (-p1) perl ($value)? "-p1":"" 60 output_option2 Print TMRCA histogram for each genealogy (-p2) perl !$run_option0 perl ($value)? "-p2":"" 60 output_option3 Print histogram of splitting times divided by prior (-p3) perl !$model_option0 perl ($value)? "-p3":"" 60 Sorry you cant use this option together with Population topology updating and estimation perl $model_option0 && $model_option3 specify_gentime Generation time in years (-u for use with -p3; default is 1) perl (defined $value) ? "-u $value":"" 1 60 specify_mutratescalar Mutation rate scalar for relevant loci -for use with -p3 (-y) perl $output_option3 perl (defined $value) ? "-y $value":"" 60 output_option4 Turn off printing estimates and histograms of population migration rate (-p4) perl ($value)? "-p4":"" 60 Please turn off extimates of 2NM (option -p4) to use a single migration parameter (-j5) perl !$output_option4 && $model_option5 output_option5 Print pairwise probabilities that one parameter is greater than another (-p5) perl ($value)? "-p5":"" 60 output_option6 Print histograms of the number of migration events (-p6) perl !$model_option0 perl ($value)? "-p6":"" 60 output_option7 Print joint estimate for splitting times (-p7) perl !$model_option0 perl ($value)? "-p7":"" 60 results *