1.3.2 A Generalized Phylogenetic Coalescent Sampler Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43 1031–1034. 2011 Phylogeny / Alignment gphocs_xsede infile Input sequence file sequences.txt gphocs_invocation perl "convertFile.sh ctrlfile.ctrl;g-phocs_1.3.2_expanse ctrlfile.ctrl" 1 gphocs_invocation3 perl " -n $numthreads -v" 80 gphocs_scheduler scheduler.conf perl "threads_per_process=$numthreads\\n" . "mem=" . (int(($numthreads)*(248/128))) . "G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 all_output All output * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) perl "runhours=$value\\n" 0.25 Maximum Hours to Run must be less than 168 perl $runtime > 168.0 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 The job will run on $numthreads processors as configured. If it runs for the entire configured time, it will consume $numthreads x $runtime cpu hours perl $runtime ne 0 Estimate the maximum time your job will need to run. We recommend testimg 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. primary_ctrlfile Select CTRL file (it must name the input file sequences.txt) ctrlfile.ctrl Plese make sure your ctrl file specifies that the seq-file name is sequences.txt perl defined $primary_ctrlfile secondary_ctrlfile Select secondary CTRL file (optional) perl defined $value ? "ctrlfile2.ctrl" : "" 3 ctrlfile2.ctrl numthreads How many threads? Sorry, threads must be no less than 6 perl $numthreads < 6 Sorry, threads must be no more than 24 perl $numthreads > 24 Please enter a thread value perl !defined $numthreads