UPP on ACCESS 4.5.1 Ultra-large alignments using Phylogeny-aware Profiles run on XSEDE Nam-phuong D. Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy Warnow Nguyen, N.-p. D., Mirarab, S., Kumar, K., et al. (2015) Ultra-large alignments using phylogeny-aware profiles. Genome Biology 16, 124 10.1186/s13059-015-0688-z Phylogeny / Alignment upp_xsede upp_invoke perl "" 0 upp_commandline perl "" 1 number_nodes perl $select_numcores < 125 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=" . (int($select_numcores*(248/32))) . "G\\n" . "threads_per_process=$select_numcores\\n" number_nodes128 perl $select_numcores > 124 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=1\\n" . "mem=243G\\n" . "threads_per_process=128\\n" infile Input File 3 perl "-s sequencefile.fa" sequencefile.fa all_results * runtime 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 1 processor as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hours perl $select_numcores <= 1 The job will run on $select_numcores processors as configured. If it runs for the entire configured time, it will consume $select_numcores X $runtime cpu hours perl $select_numcores > 1 && $select_numcores < 128 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 $select_numcores > 124 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. select_numcores Specify the number of cores 2 perl "-x $select_numcores" The number of cores must be less than or equal to 128 perl $select_numcores > 128 Please specify the number of cores perl !defined $select_numcores create_ckpfile Create a checkpoint file 4 perl ($value) ? "-cp savefile.ckp":"" out_filename Specify the name of the output file (-out_) perl ($value) ? "-o $out_filename":"" 5 Please specify an output file name perl !defined $out_filename input_params Input Parameters specify_moltype Specify the sequence type (--molecule) 6 dna amino rna dna perl "--molecule $value" Please specify the sequence type perl !defined $specify_moltype specify_ignoreoverlap Keep the backbone sequence (--ignore-overlap) 7 perl ($value ) ? "--ignore-overlap" : "" specify_configfile Specify a configuration file (-c) 8 perl (defined $specify_configfile) ? "-c configfile.conf":"" configfile.conf specify_treefile Specify an input tree file (-t) 9 perl (defined $specify_treefile) ? "-t treefile.tre":"" treefile.tre specify_fastafile Specify an input tree file (-t) 10 perl (defined $specify_fastafile) ? "-a alignment.fa":"" alignment.fa specify_backtransfile Specify a backtranslation file (-b) 11 perl (defined $specify_backtransfile ) ? "-b backtransalign.fa":"" backtransalign.fa upp_params UPP2 Run Parameters specify_decomponly Only run the decomposition step of UPP (-j) perl $which_upp 12 perl ($value) ? "--decomp_only" : "" specify_hierarchical Keep the backbone sequence (-h) 13 perl $which_upp perl ($value) ? "--heir_upp" : "" specify_adjbitscore Run with adjusted bitscore weighting (-z) perl $which_upp 14 perl ($value) ? "--bitscore_adjust" : "" specify_earlystop Run with early stop in hierarchical search (-e) perl $which_upp 15 perl ($value) ? "--early_stop" : "" decomp_params Decomposition Options specify_maxfragchunksize Maximum fragment chunk size (-F) 16 perl ($value ne $vdef) ? "-F $value":"" 999999999 specify_minpdist Minimum p-distance before stopping the decomposition (-D) 17 perl ($value ne $vdef) ? "-D $value":"" 1 specify_decompstrategy Use decomposition strategy (-S DECOMP) 18 perl ($value) ? "-S decomp":"" specify_maxtreedia Maximum tree diameter before stopping the decomposition (--diameter) 19 perl (defined $value) ? "--diameter $value":"" specify_maxalignsubset Max alignment subset size (-A) 20 perl ($value ne $vdef) ? "-A $value":"" 10 specify_nmin Only consider sequences with lengths greater than (Nmin) 21 specify_nmax Only consider sequences with lengths greater than (Nmax) 20 Please specify both Nmin and Nmax perl defined $specify_nmax && !defined $specify_nmin Please specify both Nmin and Nmax perl !defined $specify_nmax && defined $specify_nmin specify_nmanminx 23 perl defined $specify_nmin && defined $specify_nmax perl "-R N$specify_nmax N$specify_nmax" specify_medfullength Median Full Length value (-M) 24 perl (defined $value) ? "-M $value":"" Consider all fragments that are 25% longer or shorter than this value to be excluded from the backbone. If value is -1, then UPP will use the median of the sequences as the median full length specify_backbonethresh Specify a Backbone Threshold (-T) 25 perl ($value ne $vdef) ? "-T $value":"" 0.25 Please enter a value for the backbone threshold perl defined $specify_medfullength && !defined $specify_backbonethresh The value for Backbone Threshold must be greater than 0 perl $specify_backbonethresh < 0 The value for Backbone Threshold must be less than or equal to 1 perl $specify_backbonethresh > 1 Only consider sequences with lengths within (1-N)*M and (1+N)*M as full-length, where M is the median length of the full-length sequence given by the -M option and N is the percentage given by the -T option.[default: 0.25] specify_sizebackboneset Size of backbone set. (-B) 26 perl ($value ne $vdef) ? "-B $value":"" 1000 -B N, -*backboneSize N (Optional) size of backbone set. If no backbone tree and alignment is given, the sequence file will be randomly split into a backbone set (size set to N) and query set (remaining sequences), [default:min(1000,input size)]