Hi @SoilRotifer,
I got the silva files from the server that I use. I assume they obtained them from the SILVA site and used the same verion of QIIME (qiime2 2024-5) to make the qza files. I tried to do the following command
qiime rescript get-silva-data \
--p-version '138.2' \
--p-target 'SSURef_NR99' \
--o-silva-sequences silva-138.2-ssu-nr99-rna-seqs.qza \
--o-silva-taxonomy silva-138.2-ssu-nr99-tax.qza
but due to the qiime version I have access to it does not have the 138.2. I know there is a work around, but I do not have permissions to do that.
I do not think your qiime rescript edit-taxonomy will work for me. I have a problem at first with the silva-138_2-ssu-nr99-tax.qza having duplicate feature IDs. Therefore when I run the following script (regardless of the –p-mode) I get an error stating a bunch of IDs that are duplicated. This command I could not find how to remove duplicate feature IDs. I only could see how to edit the taxonomic string.
qiime rescript dereplicate --i-sequences silva-138_2-ssu-nr99-seqs_cleaned.qza --i-taxa silva-138_2-ssu-nr99-tax.qza --p-mode 'super' --o-dereplicated-sequences silva-138_2-ssu-nr99_clean-derep-super.qza --o-dereplicated-taxa silva-138_2-ssu-nr99-tax-derep-super.qza
After searching I found in order to fix this you do the below commands to remove the duplicated taxanomic values
qiime tools export --input-path silva-138_2-ssu-nr99-tax.qza --output-path silva-138_2-ssu-nr99-tax
mv taxonomy.tsv silva-138_2-ssu-nr99-tax.tsv
awk '!seen[$1]++' silva-138_2-ssu-nr99-tax.tsv > corrected_silva-138_2-ssu-nr99-tax.tsv
qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path corrected_silva-138_2-ssu-nr99-tax.tsv --output-path corrected_silva-138_2-ssu-nr99-tax.qza
I have requested for the latest version of QIIME2 to be installed on the server. I am waiting to hear.