MPboot on XSEDE 1.2 Fast maximum parsimony tree inference - run on XSEDE D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, and B.Q. Minh D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, and B.Q. Minh (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11. https://doi.org/10.1186/s12862-018-1131-3. Phylogeny / Alignment mpboot_xsede mpboot_command perl "" 0 number_nodes 2 scheduler.conf perl !$more_memory perl "ChargeFactor=1.0\\n" . "mem=4G\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" number_nodes_moremem 2 scheduler.conf perl $more_memory perl "ChargeFactor=1.0\\n" . "mem=12G\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" infile Input File perl "-s infile.txt" 10 infile.txt all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours for non-gpu; 120 for gpu jobs) 0.5 The maximum runtime for a non-gpu job can be no more than 168 hours perl $runtime > 168.0 perl "runhours=$value\\n" The job will run on 1 processors as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hours perl !$more_memory The job will run on 2 processors as configured. If it runs for the entire configured time, it will consume 4 X $runtime cpu hours perl $more_memory Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less dependably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. datatype My data set is (leave empty for auto detect) DNA AA CODON MORPH BIN auto perl ($value ne $vdef) ? "-st $value":"" 14 Specifies the data type. Leave blank for auto detect initialTree 99 Specify an initial tree (Newick format) perl (defined $value) ? "initialtree.tre":"" initialtree.tre specifyPrefix Provide a prefix for output files (-pre) perl "-pre $value" mpboot Using prefix for output files (default: alignment name). Not required 16 seed_val Enter the seed value here perl "-seed $value" 12345 14 specifyVerbose Provide verbose output (-vvv) perl "-vvv" 18 more_memory My run ran out of memory; I need more. tree_uploads Maximum Parsimony Bootstrap Approximation storeMulhits Store multiple equally parsimonious trees per bootstrap replicate (-mulhits) perl ($value) ? "-mulhits":"" 20 specifyIters Number of non-ratchet iterations before each ratchet iteration (default: 1) perl ($value ne $vdef ) ? "-ratchet_iter $value":"" 1 20 specifyRatweight Weight to add to each site selected for perturbation during ratchet (-ratchet_wgt) perl ($value ne $vdef ) ? "-ratchet_wgt $value":"" 1 24 specifyRatpercent Percentage of informative sites selected for perturbation during ratchet (-ratchet_percent) perl ($value ne $vdef ) ? "-ratchet_percent $value":"" 50 26 Default value is 50 percent turnoffRat Turn off ratchet, i.e. Only use tree perturbation (-ratchet_off) perl ($value) ? "-ratchet_off":"" 0 26 Turn off ratchet, i.e. Only use tree perturbation specifyRadius Maximum radius of SPR (-spr_rad) perl ($value ne $vdef ) ? "-spr_rad $value":"" 6 28 Default value is 6 specifyCutoff Use top #s percentile as cutoff for selecting bootstrap candidates (-cand_cutoff) perl ($value ne $vdef ) ? "-cand_cutoff $value":"" 10 30 Default value is 10 optBtreeoff Turn off refinement step on the final bootstrap tree set (-opt_btree_off) perl ($value) ? "-opt_btree_off":"" 0 30 nniHillclimb Hill-climb by NNI instead of SPR (-nni_pars) perl ($value) ? "-nni_pars":"" 0 30 uniformCost Uniform cost between character states (-cost e) perl ($value) ? "-cost e":"" 0 Sorry, you cant both specify cost and have uniform cost perl $uniformCost && defined $costFile 30 costFile Matrix of transition cost between character states (-cost) perl "-cost costfile.txt" 10 costfile.txt tree_search New Stochastic Tree Search Algorithm specifyNumpars Number of initial parsimony trees (-numpars) perl ($value ne $vdef ) ? "-numpars $value":"" 100 32 Default value is 100 specifyToppars Number of best parsimony trees (-toppars) perl ($value ne $vdef ) ? "-toppars $value":"" 20 34 Default value is 20 specifyTreeset Size of the candidate tree set (defaut: 5) perl ($value ne $vdef ) ? "-numcand $value":"" 20 36 Default value is 5 specifyPertstrength Perturbation strength for randomized NNI (-pers) perl ($value ne $vdef ) ? "-pers $value":"" 0.5 38 Default value is 0.5 specifyNumstop Number of unsuccessful iterations to stop (-numstop) perl ($value ne $vdef ) ? "-numstop $value":"" 100 40 Default value is 100 specifyIterations Run this number of iterations (-n) perl ($value ne $vdef ) ? "-n $value":"" auto 42 Default value is auto useIqp Use the IQP tree perturbation (-iqp) perl ($value) ? "-iqp":"" 0 44 useOldiqpnni Switch back to the old IQPNNI tree search algorithm (-iqpnni) perl ($value) ? "-iqpnni":"" 0 46 ultrafast_boot Ultrafast Bootstrapping useUltrafast Use Ultrafast Bootstrapping specifyUboots Specify the number of Ultrafast bootstraps. perl $useUltrafast perl "-bb $value" The number of Ultrafast bootstraps must be at least 1000 perl $useUltrafast && $specifyUboots < 1000 Please specify the number of Ultrafast bootstraps perl $useUltrafast && !defined $specifyUboots 1000 48 Default value is 5 specifyMaxiters Maximum number of iterations (-nm) perl $useUltrafast perl ($value ne $vdef) ? "-nm $value":"" 1000 50 Please specify the maximum number of iterations perl $useUltrafast && !defined $specifyMaxiters Default value is 1000 specifyUfiters Iterations for UFBoot stopping rule (-nstep) perl $useUltrafast perl ($value ne $vdef ) ? "-nstep $value":"" 100 52 Please specify the maximum number of iterations for UFBoot stopping rule perl $useUltrafast && !defined $specifyUfiters The value nstep must be 100 or greater perl $specifyUfiters < 100 The value nstep must be an even number perl (($specifyUfiters % 2) != 0) Default value is 100 specifyMincorr Minimum correlation coefficient (-bcor) perl $useUltrafast perl ($value ne $vdef ) ? "-bcor $value":"" 0.99 54 Please specify the minimum correlation coefficient (default=0.99) perl $useUltrafast && !defined $specifyMincorr Default value is 0.99 specifyRelleps RELL epsilon to break tie (-beps) perl $useUltrafast perl ($value ne $vdef ) ? "-beps $value":"" 0.5 56 Please specify the RELL epsilon (default = 0.5) perl $useUltrafast && !defined $specifyRelleps Default value is 0.5 consensusReconstruction Consensus Reconstruction consensusTrees Set of input trees for consensus reconstruction perl (defined $consensusTrees) ? "consensustrees.tre":"" consensustrees.tre 99 specifyMinsplit Min split support (-t) perl defined $consensusTrees perl ($value ne $vdef) ? "-t $value":"" 60 0 The Min split support value must be between 0 and 1 perl $specifyMinsplit < 0 || $specifyMinsplit > 1 Please enter a value for Min split support; must be between 0 and 1 perl !defined $specifyMinsplit Must be between 0 and 1, use 0.5 for majority-rule specifyBurnin How many trees to discard at beginning of treefile (-bi) perl defined $consensusTrees perl (defined $value) ? "-bi $value":"" 62 writeTocontree Compute consensus tree to .contree file (-con) perl defined $consensusTrees perl ($value) ? " -con ":"" 64 writeTonexnet Compute consensus network to .nex file (-net) perl defined $consensusTrees perl ($value) ? " -net ":"" 64 assignSupportvals Assign support values for this file to .suptree (-sup) perl defined $consensusTrees perl (defined $value) ? "-sup target_tree.tre":"" target_tree.tre 66 robinsonFoulds Robinson-Foulds distance rfTreefile Specify a tree set for RF distances rftreefile.tre 99 alltoallRfdistance Compute all-to-all RF distances of trees in treefile (-rf_all) perl defined $rfTreefile perl ($value) ? "-rf_all rftreefile.tre":"" 68 Default value is 5 computeRfadj Compute RF distances of adjacent trees in treefile (-rf_adj) perl defined $rfTreefile perl ($value) ? "-rf_adj rftreefile.tre":"" 72 rfdistTwosets Compute all RF distances between two sets of trees (-rf treefile2) perl defined $rfTreefile perl (defined $value) ? "-rf rftreefile2.tre":"" rftreefile2.tre 70 generateRandom Generate Random Trees randomTreemodel Create a random tree under this model (-r) -r -ru -rcat -rbal -rcsg -r "-r $specifyTaxa" -ru "-ru $specifyTaxa" -rcat "-rcat $specifyTaxa" -rbal "-rbal $specifyTaxa" -rcsg "-rcsg $specifyTaxa" 74 specifyTaxa How many taxa in your random trees? perl defined $randomTreemodel 76 specifyLengths perl (defined $specifyminLengths) ? "-rlen $specifyminLengths $specifymeanLengths $specifymaxLengths":"" 76 specifyminLengths Min branch lengths of random trees specifymeanLengths Mean branch lengths of random trees Please specify the mean branch length perl defined $specifyminLengths && !defined $specifymeanLengths specifymaxLengths Max branch lengths of random trees Please specify the max branch length perl defined $specifyminLengths && !defined $specifymaxLengths randomTrees perl (defined $randomTreemodel ) ? "randomtrees.tre":"" randomtrees.tre 99