otc-degree-distribution /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/exemplified_phylo/regraft_cleaned_ott.tre > /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/taxonomy_degree_distribution.txt otc-degree-distribution \ /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/labelled_supertree/labelled_supertree.tre \ > /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/supertree_degree_distribution.txt otc-tree-tool \ /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/labelled_supertree/labelled_supertree.tre \ --lost-taxa-vs=/home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/exemplified_phylo/regraft_cleaned_ott.tre \ --taxonomy=/home/bredelings/Devel/OpenTree/ott-3.0 \ > /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/.lost_taxa.txt \ || rm /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/.lost_taxa.txt mv /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/.lost_taxa.txt /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/lost_taxa.txt ./bin/combine_ott_cleaning_logs.py \ /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/cleaned_ott/cleaned_ott_1.json \ /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/cleaned_ott/cleaned_ott_pruned_nonflagged.json \ /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/cleaned_ott/cleaned_ott.json ./bin/run_assessments.py /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5 /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/summary.json 2>&1 | tee /home/bredelings/Devel/OpenTree/synth-runs/v10.3-5/assessments/log.txt || true "NONE" is an invalid formatter name