Error: unknown sequence format for Augur tree

Help and Getting Started
1

Hi Sir, I am the new user for using the nextstrain. Following the website’s instruction, I tried to type the below command to build the phylogenetic tree using the iqtree model. But the system showed that I used the unknown sequence format. The fasta file I used here was actually aligned by ClusterW on MEGA X11. Is this file not recognized by Augur? Can anyone help to explain it？ As the help page only mentioned that this format needed to be fasta or VCF. I am a bit confused. Thanks!

$ augur tree --method iqtree --alignment HA_H1N1_61samples_2019.fas --substitution-model auto --output HA_H1N1_ML_tree --tree-builder-args=“-czb”

2

Hi @Emma316, welcome. Any aligned fasta, regardless of the aligner, should be fine to pass into augur tree. Can you copy and paste the exact error message and other output that shows when you run your command above?

3

Hi trs, sorry that I just realized I missed this message before! I figured it out! It seems that *.fas file can’t be read by iqtree. Once I transfer the *.fas file to *.fasta file, it worked.