Missing part of gene in Diversity figure on Auspice.us

Help and Getting Started
#1

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!

screenshot
screenshot1615×330 15.2 KB

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)

#2

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.

#3

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.

#4

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.