I have a .vcf of a bacteria but when I try and make a tree in augur I get an error from the numpy pacakage, which I don’t know how to address.
augur tree \
Traceback (most recent call last):
File “/conda/envs/nextstrain/bin/augur”, line 10, in
File “/conda/envs/nextstrain/lib/python3.8/site-packages/augur/main.py”, line 10, in main
return augur.run( argv[1:] )
File “/conda/envs/nextstrain/lib/python3.8/site-packages/augur/init.py”, line 75, in run
File “/conda/envs/nextstrain/lib/python3.8/site-packages/augur/tree.py”, line 451, in run
variable_fasta = write_out_informative_fasta(compress_seq, args.alignment, stripFile=args.exclude_sites)
File “/conda/envs/nextstrain/lib/python3.8/site-packages/augur/tree.py”, line 333, in write_out_informative_fasta
align = np.rot90(sites)
File “<array_function internals>”, line 180, in rot90
File “/conda/envs/nextstrain/lib/python3.8/site-packages/numpy/lib/function_base.py”, line 223, in rot90
raise ValueError(“Axes must be different.”)
ValueError: Axes must be different.
Thank you for your help