# Error: unknown sequence format for Augur tree

**URL:** <https://nextstrain.discourse.group/t/error-unknown-sequence-format-for-augur-tree/1188>\
**Category:** Help and Getting Started\
**Created:** [July 18, 2022, 4:05am UTC](https://nextstrain.discourse.group/t/error-unknown-sequence-format-for-augur-tree/1188 "2022-07-18T04:05:04Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Emma316](https://avatars.discourse-cdn.com/v4/letter/e/a3d4f5/32.png) [@Emma316](https://nextstrain.discourse.group/u/Emma316)\
**Post date:** [July 18, 2022, 4:05am UTC](https://nextstrain.discourse.group/t/error-unknown-sequence-format-for-augur-tree/1188/1 "2022-07-18T04:05:04Z")

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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”

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**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\
**Post date:** [July 18, 2022, 5:22pm UTC](https://nextstrain.discourse.group/t/error-unknown-sequence-format-for-augur-tree/1188/2 "2022-07-18T17:22:27Z")

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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?

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**Author:** ![Emma316](https://avatars.discourse-cdn.com/v4/letter/e/a3d4f5/32.png) [@Emma316](https://nextstrain.discourse.group/u/Emma316)\
**Post date:** [March 27, 2024, 10:41am UTC](https://nextstrain.discourse.group/t/error-unknown-sequence-format-for-augur-tree/1188/3 "2024-03-27T10:41:28Z")

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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.