This script is intended to filter reference sequences based on the length of that sequence given the taxonomy provided, and leave the rest of the data as is. That is, your command would only filter Bacteria based on the length you specified, all other data will remain in your final output file. This is why I recommended
qiime taxa filter-seqs.
If you would like to use
qiime rescript filter-seqs-length-by-taxon, then you could use the following command by just setting impossibly high sequence lengths for the other taxonomic groups. But this would end up being much slower than the command I recommended as it will have to check the taxonomy of each entry, and then check the sequence length before it makes the decision to filter.
qiime rescript filter-seqs-length-by-taxon \
–i-sequences silva-138-ssu-nr99-seqs-cleaned.qza \
–i-taxonomy silva-138-ssu-nr99-tax.qza \
–p-labels Bacteria Archaea Eukaryota \
–p-min-lens 1200 9999 9999 \
–o-filtered-seqs silva-138-ssu-nr99-seqs-filt.qza \