1 Phylogenetic tree-based annotation of proteins Haiming Tang, Robert D Finn, Paul D Thomas, Haiming Tang, Robert D Finn, Paul D Thomas, TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations, Bioinformatics, Volume 35, Issue 3, 01 February 2019, Pages 518–520, https://doi.org/10.1093/bioinformatics/bty625 Phylogeny / Annotation tree_grafter treegrafter_comet perl "" 0 number_threads 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=$num_cpus\\n" invoke_treegrafter 5 perl $which_treegrafter < 4 perl "perl /projects/ps-ngbt/opt/comet/treegrafter/TreeGrafter/treeGrafter.pl" invoke_treegrafter2 5 perl $which_treegrafter == 4 perl "perl /projects/ps-ngbt/opt/comet/treegrafter/TreeGrafter/treeGrafter_verbose.pl" test_db 50 perl $which_treegrafter == 1 perl "-d /projects/ps-ngbt/opt/comet/treegrafter/TreeGrafter-master/Test/PANTHER_mini" panther_db15 50 perl $which_treegrafter == 2 perl "-d /projects/ps-ngbt/opt/comet/treegrafter/PANTHER15.0_data -algo hmmscan" panther_db141 50 perl $which_treegrafter > 2 perl "-d /projects/ps-ngbt/opt/comet/treegrafter/PANTHER14.1_data -algo hmmscan" infile Input File (query) perl "-f treegrafter.fasta" 10 treegrafter.fasta all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) perl "runhours=$value\\n" 168 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 The job will run on $num_cpus processors as configured. If it runs for the entire configured time, it will consume num_cpus X $runtime cpu hours perl $runtime > 0 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. which_treegrafter Choose your TreeGrafter database 1 Test Version 3 Panther V. 14.1 2 Panther V. 15.0 4 Panther V. 14.1 verbose 3 Please choose a TreeGrafter database perl !defined $which_treegrafter 4 num_cpus How many cpus? 1 37 Please enter a number of threads 1-24 perl !defined $num_cpus Please enter a number of threads 24 or less perl $num_cpus > 24 Please enter a number of threads 1 or more perl $num_cpus < 1 output_name Name your output file perl "-o $value" 35 num_cpus2 How many cpus? perl (defined $value) ? "-cpus $value":"" 1 70 Please enter a number of threads 24 or less perl $num_cpus2 > 24