cat /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/nonempty_trees.txt \ | sed -e "s:^:/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/:g" \ > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/scratch/args.txt ./bin/run-subproblem-finder.sh \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/scratch \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/dumped-subproblem-ids.txt \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/contesting-trees.json \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/taxonomy.tre \ -f/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/scratch/args.txt bash bin/checksum-tree-files.sh \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/scratch \ && \ cp /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/dumped-subproblem-ids.txt \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/checksummed-subproblem-ids.txt /home/bredelings/Devel/OpenTree/propinquity bash bin/move-subproblem-if-differing.sh \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/scratch \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/checksummed-subproblem-ids.txt \ && \ cp /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/checksummed-subproblem-ids.txt \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/subproblem-ids.txt otc-taxonomy-parser /home/bredelings/Devel/OpenTree/ott-3.0 --config=/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/config \ --in-tree=/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/taxonomy.tre \ --any-flag=incertae_sedis,major_rank_conflict,unplaced,unclassified \ --format="%I" \ > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/incertae_sedis.txt for n in $(cat /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/subproblem-ids.txt) ; do \ id=${n%.tre} ; \ otc-solve-subproblem \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/$n \ -n${id} \ -I /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/incertae_sedis.txt \ > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblem_solutions/${n} ; \ done ; cp /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblems/subproblem-ids.txt \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblem_solutions/solution-ids.txt sed "s:^:/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblem_solutions/:" \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblem_solutions/solution-ids.txt \ > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblem_solutions/paths.txt otc-graft-solutions -f/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblem_solutions/paths.txt \ > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/grafted_solution/.grafted_solution.tre && \ mv /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/grafted_solution/.grafted_solution.tre \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/grafted_solution/grafted_solution.tre rm /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/subproblem_solutions/paths.txt otc-unprune-solution-and-name-unnamed-nodes \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/grafted_solution/grafted_solution.tre \ /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/regraft_cleaned_ott.tre \ -i/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/incertae_sedis.txt \ -j/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/labelled_supertree/broken_taxa.json \ -s/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/labelled_supertree/input_output_stats.json \ > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/labelled_supertree/labelled_supertree.tre