otc-degree-distribution \
		../opentree8.0/exemplified_phylo/taxonomy.tre \
		> ../opentree8.0/exemplified_phylo/pruned_taxonomy_degree_distribution.txt
cat ../opentree8.0/exemplified_phylo/pruned_taxonomy_degree_distribution.txt \
		| head -n2 \
		| tail -n1 \
		| awk '{print "{\"x\": " $2 "}" }' \
		> ../opentree8.0/annotated_supertree/num_phylo_tips.json
otc-annotate-synth \
		../opentree8.0/labelled_supertree/labelled_supertree.tre \
		$(sed "s:^:../opentree8.0/exemplified_phylo/:" ../opentree8.0/exemplified_phylo/nonempty_trees.txt) \
		> ../opentree8.0/annotated_supertree/preannotations1.json
bin/add_subproblem_info_to_annotations.py \
		../opentree8.0/subproblems/subproblem-ids.txt \
		../opentree8.0/annotated_supertree/preannotations1.json \
		../opentree8.0/annotated_supertree/annotations1.json
bin/gen_attributes.py ../opentree8.0/config /Users/karen/.opentree --out-dir=../opentree8.0 \
		> ../opentree8.0/annotated_supertree/preannotations2.json
bin/merge-json.py \
		../opentree8.0/annotated_supertree/num_phylo_tips.json \
		x \
		../opentree8.0/annotated_supertree/preannotations2.json \
		num_leaves_in_exemplified_taxonomy \
		> ../opentree8.0/annotated_supertree/annotations2.json
bin/merge-json.py \
		../opentree8.0/annotated_supertree/annotations1.json \
		../opentree8.0/annotated_supertree/annotations2.json \
		> ../opentree8.0/annotated_supertree/annotations.json