Hello Shuqi,
As you have noticed, most of the QIime2 tutorials use 16S V4 data, but there are plugins for working with shotgun data just like you have! Check out q2-shogun and this discussion of upcoming shotgun data support within Qiime2.
Your import and quality control looks good! OTU clustering was built for amplicons, so it may not be a great fit for shotgun reads.