Hi, Yoha!
I am not an expert in R. From log I can see you need to transpose your OTU-table, so that that sequences are recorded in rows, and sample-ids in columns.
As I understand from your code, you need to choose only one line to define otu variable correctly, and you have two to choose from. The second one replaces the first definition of the otu. Choose one and see which one does the work.
Then redo the steps you've done before through QIIME2 and it should work.
Cheers,