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Initially, the workflow failed with the following error: ``` Error: 0: When reading genome annotation 1: When reading file: "config/hku1/genemap.gff" 2: Attempted to parse the genome annotation as JSON and as GFF, but both attempts failed: JSON error: invalid type: string "NC_006577.2\tfeature\tsource\t1\t29926\t.\t+\t.\tgene=nuc NC_006577.2\tfeature\tgene\t206\t13600 \t.\t+\t.\tgene=ORF1a NC_006577.2\tfeature\tgene\t13600\t21753\t.\t+\t.\tgene=ORF1b NC_006577.2\tfeature\tgene\t21773\t22933\t.\t+\t.\tg ene=HE NC_006577.2\tfeature\tgene\t22942\t27012\t.\t+\t.\tgene=Spike NC_006577.2\tfeature\tgene\t22978\t25221\t.\t+\t.\tgene=S1 NC_00657 7.2\tfeature\tgene\t27051\t27380\t.\t+\t.\tgene=S2 NC_006577.2\tfeature\tgene\t27051\t27380\t.\t+\t.\tgene=ORF4 NC_006577.2\tfeature\tge ne\t27373\t27621\t.\t+\t.\tgene=E NC_006577.2\tfeature\tgene\t27633\t28304\t.\t+\t.\tgene=M NC_006577.2\tfeature\tgene\t28320\t29645\t.\ t+\t.\tgene=N NC_006577.2\tfeature\tgene\t28342\t28959\t.\t+\t.\tgene=N2", expected struct GeneMap at line 2 column 1 GFF3 error: When processing gene, 'N': When processing feature group 'N' ('N') of type 'gene': genes must consist of exactly one f eature: Expected exactly one element, but found: 2 2: Location: /workdir/packages/nextclade/src/gene/gene_map.rs:56 ``` While looking at the referenced file, and comparing it to the other `genemap.gff` files in the config, I noticed that all the others used `gene_name` for everything after the first `gene` line. I changed this file to match, and the workflow got past the point where it was previously erroring out. I have no idea why this worked; hopefully somebody will explain in the code review.
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