I think I found the issue; do you think the presence of some adapter sequences may be interfering? Some fastq files have between 10% of sequences as adaptors and some samples have as high as 20% sequences corresponding to adapters.
I usually only run fastQC, cutadapt, trimmomatic, etc. on RNA sequencing data. This is the first time I had to do this for a 16S sequencing pipeline.
I think besides the adapters I should be good. I will try to fix the problematic files.
