Analyzing whole-metagenomic shotgun sequencing data with V4 amplicon sequence data

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@Introducing Greengenes2 2022.10

If you have shotgun metagenomic data

We recommend processing the short read data using the Woltka toolkit, against version 2 of the Web of Life database (WoLr2 can be found here). After processing your short reads with Woltka, you can use the resulting FeatureTable[Frequency] with the filter-features action of q2-greengenes2. A FeatureData[Taxonomy] artifact can then be generated using the taxonomy-from-table action.

Please can you just tell me how could I use Woltka? Because they just told me to pre-process the data first. I just downloaded whole genome sequence data from the SRA database using the fondue plugin. But what I'm seeing in the Woltka tutorial they have used a .qza file against a taxonomy.qza file.

qiime woltka classify \
  --i-alignment align_sam.qza \
  --p-target-rank genus \
  --i-reference-taxonomy taxonomy.qza \
  --o-classified-table table.qza

But I don't have that file yet. Then how could I use Woltka to pre-process my shotgun sequence data?