otc-degree-distribution \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/taxonomy.tre \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/pruned_taxonomy_degree_distribution.txt
cat /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/pruned_taxonomy_degree_distribution.txt \
	| head -n2 \
	| tail -n1 \
	| awk '{print "{\"x\": " $2 "}" }' \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/num_phylo_tips.json
otc-annotate-synth \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/labelled_supertree/labelled_supertree.tre \
	$(sed "s:^:/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/:" /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/nonempty_trees.txt) \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/preannotations1.json
bin/add_subproblem_info_to_annotations.py \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/subproblem-ids.txt \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/preannotations1.json \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/annotations1.json
bin/gen_attributes.py /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/config /home/bredelings/.opentree --out-dir=/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4 \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/preannotations2.json
bin/merge-json.py \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/num_phylo_tips.json \
	x \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/preannotations2.json \
	num_leaves_in_exemplified_taxonomy \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/annotations2.json
bin/merge-json.py \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/annotations1.json \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/annotations2.json \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/annotated_supertree/annotations.json