Hi - I’ve found discussion of this scattered over several help topics and GitHub issues, but am having trouble figuring out what action I should take. I am running the default ncov workflow with very minor modifications, not interested in doing extensive customization, but I would like to get bootstrap values in order to be able to annotate the nodes of my tree. (I would preferably like these to be present in the newick file itself, not in the auspice json output, since I’m not going to use auspice for my publication figures). My questions are 1) are the node support values already present somewhere in the results of running the default workflow? (Just to make sure I’m not missing something) And if not…2) how do I modify the workflow to get them?
I tried following this: Enable bootstrap support by huddlej · Pull Request #839 · nextstrain/augur · GitHub to modify my default parameters.yaml file to say
--tree-builder-args '-bb 1000 -bnni -czb' and
override-default-args: true but I get the following error message on the augur tree step:
augur tree --alignment results/filtered.fasta --tree-builder-args '-bb 1000 -bnni -czb' --exclude-sites defaults/sites_ignored_for_tree_topology.txt --output results/tree_raw.nwk --nthreads 8 2>&1 | tee logs/tree.txt --override-default-args ERROR: Shell exited 2 when running: iqtree2 -nt 8 -s results/masked_filtered-delim.fasta -m GTR -ninit 2 -n 2 -me 0.05 -bb 1000 -bnni -czb > results/masked_filtered-delim.iqtree.log Command output was: Ultrafast bootstrap does not work with -fast, -te or -n option 7 masking sites read from defaults/sites_ignored_for_tree_topology.txt Building a tree via: iqtree2 -nt 8 -s results/masked_filtered-delim.fasta -m GTR -ninit 2 -n 2 -me 0.05 -bb 1000 -bnni -czb > results/masked_filtered-delim.iqtree.log Nguyen et al: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300 ERROR: TREE BUILDING FAILED Please see the log file for more details: results/masked_filtered-delim.iqtree.log Building original tree took 0.7982666492462158 seconds
The masked_filtered-delim.iqtree.log file is empty.
What else do I need to modify in order for the workflow to give me bootstrap values?
I’m still constantly learning new things about how Nextstrain works so apologies if my understanding of something is off-base.