I selected “Keep existing gene calls” and uploaded a GenBank file, but RAST failed with the cryptic error “Zero-size or non-existent FASTA file.” What does this mean?
• Most likely it means that your GenBank file contains either: • “Gene” entries but no “CDS” entries, or • “CDS” entries lacking a “/translation=” field. • Because the GenBank format tolerates many exception conditions that make unambiguous translation of a gene into protein sequence difficult (such as “fuzzy” gene boundaries, frameshifts at unspecified locations, and the notion of “conceptual translations”), and because the GenBank format does not clearly indicate when embedded STOP codons should be translated as selenocystine or pyrrolysine, the SEED GenBank parser used by RAST expects genes to be specified by “CDS” entries complete with explicit “/translation=” fields. The unqualified “gene” entry, with only location and name information, but no sequence information, leaves RAST uncertain about how the gene should be translated into protein sequence.
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