"Sequence Duplication Levels" module still fails after pre-processing Illumina data
FastQC assumes that all samples are for whole genome sequencing and will flag them as failed if they differ too much from that assumption. This will, for example, cause essentially all RNA-seq, ChIP-seq, and ATAC-seq samples to fail in one module or another. This is not any cause for concern and is completely expected. Primarily concern yourself with whether all of your samples are similar in their metrics.