I am trying to combine my feature table and taxonomy.tsv. I have done this previously without issue. I have just updated my version of qiime to 2026.4.
my taxonomy.tsv file looks fine, i.e. the taxonomy of top couple of entries;
d__Bacteria;p__Thermodesulfobacteriota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella;s__uncultured_bacterium
d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas
d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiia;o__Pedosphaerales;f__Pedosphaeraceae;g__Ellin516;s__uncultured_bacterium
however, when i combine the two files, the taxonomy column has semi-colons entered between every character. i think it's similar to this issue, from a while ago; Taxa names (each letter) are separated by semicolons after merging feature-table and taxonomy
here is the first few entries in this combined tsv
d; _; _; B; a; c; t; e; r; i; a; ;; p; _; _; T; h; e; r; m; o; d; e; s; u; l; f; o; b; a; c; t; e; r; i; o; t; a; ;; c; _; _; S; y; n; t; r; o; p; h; i; a; ;; o; _; _; S; y; n; t; r; o; p; h; a; l; e; s; ;; f; _; _; S; m; i; t; h; e; l; l; a; c; e; a; e; ;; g; _; _; S; m; i; t; h; e; l; l; a; ;; s; _; _; u; n; c; u; l; t; u; r; e; d; _; b; a; c; t; e; r; i; u; m
d; _; _; B; a; c; t; e; r; i; a; ;; p; _; _; P; s; e; u; d; o; m; o; n; a; d; o; t; a; ;; c; _; _; G; a; m; m; a; p; r; o; t; e; o; b; a; c; t; e; r; i; a; ;; o; _; _; P; s; e; u; d; o; m; o; n; a; d; a; l; e; s; ;; f; _; _; P; s; e; u; d; o; m; o; n; a; d; a; c; e; a; e; ;; g; _; _; P; s; e; u; d; o; m; o; n; a; s
d; _; _; B; a; c; t; e; r; i; a; ;; p; _; _; V; e; r; r; u; c; o; m; i; c; r; o; b; i; o; t; a; ;; c; _; _; V; e; r; r; u; c; o; m; i; c; r; o; b; i; i; a; ;; o; _; _; P; e; d; o; s; p; h; a; e; r; a; l; e; s; ;; f; _; _; P; e; d; o; s; p; h; a; e; r; a; c; e; a; e; ;; g; _; _; E; l; l; i; n; 5; 1; 6; ;; s; _; _; u; n; c; u; l; t; u; r; e; d; _; b; a; c; t; e; r; i; u; m
code used for the combining;
biom add-metadata -i taxonomy/Metataxa/feature-table.biom -o taxonomy/Metataxa/filtered_table_with_taxonomy.biom --observation-metadata-fp taxonomy/taxonomy.tsv --sc-separated taxonomy
biom convert -i taxonomy/Metataxa/filtered_table_with_taxonomy.biom -o taxonomy/Metataxa/filtered_table_with_taxonomy.tsv --to-tsv --header-key Taxon
any thoughts? it's surmountable with some excel or coding magic, but it's just weird! i did the exact same set of code only a couple of weeks ago, although on a older version of qiime, without issue.