I am running in Docker on Windows and I have run through the tutorials, which worked fine. Now I am trying to run Nextstrain with a collection of flu sequences and I’m getting stuck on this command (as in the tutorial):
augur align
–sequences results/filtered.fasta
–reference-sequence config/flu_outgroup.gb
–output results/aligned.fasta
–fill-gaps
I have a file flu_outgroup.gb from Genbank, but I consistently get the following error: ERROR: Cannot read reference sequence. make sure the file config/flu_outgroup.gb contains one sequence in genbank or fasta format. I’ve read through this documentation and I think my reference looks okay based on that guidance. I’ve tried it with another reference sequence in FASTA format and get the same result. Can you provide any insight into why this reference sequence isn’t working?
flu_outgroup.gb (30.8 KB)
Thank you.