otc-degree-distribution \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/taxonomy.tre \ > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/pruned_taxonomy_degree_distribution.txt cat /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/pruned_taxonomy_degree_distribution.txt \ | head -n2 \ | tail -n1 \ | awk '{print "{\"x\": " $2 "}" }' \ > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/num_phylo_tips.json otc-annotate-synth \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/labelled_supertree/labelled_supertree.tre \ $(sed "s:^:/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/:" /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/nonempty_trees.txt) \ > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/preannotations1.json bin/add_subproblem_info_to_annotations.py \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/subproblem-ids.txt \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/preannotations1.json \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/annotations1.json bin/gen_attributes.py /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/config /Users/karen/.opentree --out-dir=/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1 \ > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/preannotations2.json bin/merge-json.py \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/num_phylo_tips.json \ x \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/preannotations2.json \ num_leaves_in_exemplified_taxonomy \ > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/annotations2.json bin/merge-json.py \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/annotations1.json \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/annotations2.json \ > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/annotated_supertree/annotations.json