Augur tree error from numpy need help to fix

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 \

–alignment data/NK_gvh.vcf
–vcf-reference data/ref.fasta
–method iqtree
–output results/tree_raw.nwk
–nthread 5
Traceback (most recent call last):
File “/conda/envs/nextstrain/bin/augur”, line 10, in
File “/conda/envs/nextstrain/lib/python3.8/site-packages/augur/”, line 10, in main
return argv[1:] )
File “/conda/envs/nextstrain/lib/python3.8/site-packages/augur/”, line 75, in run
File “/conda/envs/nextstrain/lib/python3.8/site-packages/augur/”, 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/”, 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/”, line 223, in rot90
raise ValueError(“Axes must be different.”)
ValueError: Axes must be different.

Thank you for your help

Sorry for the late reply. Could you share the data with me so that I can have a look? Either upload/post a link here or send me an email to cornelius.roemer at and I’ll try to see what the problem is if you haven’t figured it out in the meantime.