RAST is complaining about “Duplicate contig IDs,” but all my contig IDs appear unique to me. Whats going on?
• Usually, this is because your contig IDs contain “whitespace” characters. The FASTA standard specifies that the header must not contain “whitespace” between the “>” symbol and the contig ID, and that everything after the first “whitespace” character is a “comment,” and not part of the identifier. Thus, the first FASTA header below is invalid (no ID, just comment), while the following two will be interpreted as a pair of “duplicate IDs,” that are both named “B.”: > E. coli main chromosome >B. subtilis main chromosome >B.
