Missing part of gene in Diversity figure on Auspice.us

Hello community,

I am running augur to build phylogentic tree and want to visualize it on Auspice.us. Now there is a problem with my Diversity figure on Auspice.us that a part of gene, the “ORF1b”, is missing. Instead, there is a gene “ORF1ab” but in a wrong position, which is at 266…13468 but should stand at 266…21555). What should I do to modify the “ORF1ab” to right position or add “ORF1a” and “ORF1b” seperately? Any advices are valueable for me since I am a very green-hand on this.

Here are the screenshot and reference sequence used in Augur code. If any more info. needed please reply to me. Many thanks to every assistance!

Reference sequence download from NCBI named NC_045512_e.gb (Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, co - Nucleotide - NCBI)
(sry I can not upload it due to characters limitation)

The file name with a “_e” because I edit the file and delete every line of "/locus_tag=“GU280_gpxx” since it takes place of the gene name in Auspice.us filter. I think it has no relationship with this missing but just in case it has.

Would need to see your .json file, this should be encoded in “genome_annotations”

You should use the reference.gb from ncov/defaults at master · nextstrain/ncov · GitHub as augur is probably messing with the frameshift of ORF1ab in yours.
Maybe try Snakemake --cores 1 -R translate
to not redo all the build after changing the reference.gb.

Thank you @babarlelephant . I change my ref seq to the one on Git nextstrain and now the missing part has been added. I also checked the .json file and find it combine the ORF1ab as a whole gene and define it in a wrong position. I have no idea how this happen since I use the file download from NCBI and only delete several lines useless.