Hi @airbender97,
It looks like you're using the PairedEndFastqManifestPhred64V2 and the error says the decoded Phred score is out of range.
If you go back to the documentation, is there anyother manifest format you coudl try that might addres that Phred score differently?
Quality filtering is DADA2's second step. There's also an entire quality filtering plugin (q2-quality-filtering). Although the DADA2 plugin and quality filtering plugin shouldn't be combined because again, DADA2 makes assumptions that its not getting quality filtered data.
Best,
Justine