otc-degree-distribution /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/regraft_cleaned_ott.tre > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/taxonomy_degree_distribution.txt
otc-degree-distribution \
	/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/labelled_supertree/labelled_supertree.tre \
	> /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/supertree_degree_distribution.txt
otc-tree-tool \
  /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/labelled_supertree/labelled_supertree.tre \
  --lost-taxa-vs=/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/exemplified_phylo/regraft_cleaned_ott.tre \
  --taxonomy=/home/bredelings/Devel/OpenTree/ott-3.0 \
  > /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/.lost_taxa.txt \
  || rm /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/.lost_taxa.txt
mv /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/.lost_taxa.txt /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/lost_taxa.txt
./bin/combine_ott_cleaning_logs.py \
	/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/cleaned_ott/cleaned_ott_1.json \
	/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/cleaned_ott/cleaned_ott_pruned_nonflagged.json \
	/home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/cleaned_ott/cleaned_ott.json
./bin/run_assessments.py /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2 /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/summary.json 2>&1 | tee /home/bredelings/Devel/OpenTree/synth-runs/opentree10.2/assessments/log.txt || true
"NONE" is an invalid formatter name
MONOPHYLY_TEST_CSV_FILE is not in the env, so no monophyly tests are being run