Hi, I am visualizing using a small set of sequences and my json file for traits (augur traits command) shows null value for each sequence. Am i supposed to manually input the values in the json file? how does this work? I can visualize in auspice but it shows no variable except the name of the sequence and it’s divergence and coalscent which is obviously there after the augur tree refine command…
alignment1.fasta (327.0 KB)
metadata.tsv (15.2 KB)
traits.json (8.9 KB)
Hi! Can you share the exact
augur traits command you’re running? That would help me understand what’s going on here.
hi, yes :
augur refine --tree tree1.nwk --alignment alignment2.fasta --metadata metadata1.tsv --output-tree tree2.nwk --output-node-data branch_length.json --timetree --coalescent opt --date-confidence --date-inference marginal --clock-filter-iqd 4 --keep-polytomies