QIIME2-Compatible Database for AMF Taxonomy Assignment – Issues with SILVA Lineage Depth

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Hi @Salma_Sarker,

It is far easier to make use of qiime rescript get-silva-data .... If you do not require the sequences you can simply run the following:

qiime rescript get-silva-data \
    --p-version 138.2 \
    --p-target SSURef_NR99 \
    --p-ranks domain phylum class order family genus \
    --p-no-download-sequences \
    --output-dir ./silva-138.2-output \
    --verbose

The --p-no-download-sequences flag will not download any sequences... but will result in an empty QZA sequence file. Run qiime rescript get-silva-data --help to check out other options. Note this action essentially wraps the silva taxonomy parser.

If you need to modify the taxonomy output checkout qiime rescript edit-taxonomy ....

-Hope this helps!

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