cat /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/nonempty_trees.txt \
| sed -e "s:^:/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/:g" \
> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/scratch/args.txt
./bin/run-subproblem-finder.sh \
  /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/scratch \
  /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/dumped-subproblem-ids.txt \
  /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/contesting-trees.json \
  /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/taxonomy.tre \
  -f/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/scratch/args.txt
bash bin/checksum-tree-files.sh \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/scratch \
&& \
	cp /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/dumped-subproblem-ids.txt \
	   /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/checksummed-subproblem-ids.txt
/home/bredelings/Devel/OpenTree/propinquity
bash bin/move-subproblem-if-differing.sh \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/scratch \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/checksummed-subproblem-ids.txt \
&& \
	cp /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/checksummed-subproblem-ids.txt \
	   /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/subproblem-ids.txt
otc-taxonomy-parser /home/bredelings/Devel/OpenTree/ott-3.0 --config=/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/config \
  	--in-tree=/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/taxonomy.tre \
	--any-flag=incertae_sedis,major_rank_conflict,unplaced,unclassified \
	--format="%I" \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/incertae_sedis.txt
for n in $(cat /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/subproblem-ids.txt) ; do \
	id=${n%.tre} ; \
	otc-solve-subproblem \
		/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/$n \
		-n${id} \
		-I /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/incertae_sedis.txt \
		> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblem_solutions/${n} ; \
done ;
cp /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblems/subproblem-ids.txt \
   /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblem_solutions/solution-ids.txt
sed "s:^:/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblem_solutions/:" \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblem_solutions/solution-ids.txt \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblem_solutions/paths.txt
otc-graft-solutions -f/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblem_solutions/paths.txt \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/grafted_solution/.grafted_solution.tre && \
mv /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/grafted_solution/.grafted_solution.tre \
   /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/grafted_solution/grafted_solution.tre
rm /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/subproblem_solutions/paths.txt
otc-unprune-solution-and-name-unnamed-nodes \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/grafted_solution/grafted_solution.tre \
	/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/regraft_cleaned_ott.tre \
	-i/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/exemplified_phylo/incertae_sedis.txt \
	-j/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/labelled_supertree/broken_taxa.json \
	-s/home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/labelled_supertree/input_output_stats.json \
	> /home/bredelings/Devel/OpenTree/synth-runs/v10.3-4/labelled_supertree/labelled_supertree.tre