What happens when 2 genomes have the same name but different sequences?

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1

My understanding is that Nextstrain will remove duplicates from the input datasets by looking at both sequence names and the actual sequences. What happens if 2 sequences have the same name but different sequences? Will the run fail or just throw a warning?

A related question is that Nextstrain will strip the “hCoV-19/” from sequence names. Does that happen for all input data, and before de-duplication?

We use the latest master branch.

Thank you for such a useful tool and great support to the users!

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Answering myself: if 2 sequences have both identical name and sequence, the duplicate will be removed quietly; if 2 sequences have identical name but different sequences, only the first one will be keep, and if user set error_on_duplicates=True, the names will be written into a record.
Reference ncov code

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