Hello scientific community... I was running the following command "filterAndTrim" with default parameters for trimming of 16s data in DADA2 pipeline it worked fine. The only problem I have is that it is trimming more than 95% of my reads for all samples why it is happening can anyone tell?

My Fastaq files are taken without any trimming into third-party software like cutadapt, fastp or trimmomatic. If all the reads are got trimmed how can I proceed with so little reads. Any guidance? I also tried to cut the bad sequences from the end of the sequence then most of the reads were filtered out.

out <- filterAndTrim(dataF, filt.dataF, dataR, filt.dataR, truncLen=0,
                     maxN=0, maxEE=Inf, truncQ=2, rm.phix=TRUE,
                     compress=FALSE, multithread=FALSE)

head(out) -

                    reads.in reads.out
AIJ_R1.fastq    63023      1565
AIZ_R1.fastq   104880      2593
AOJ_R1.fastq    76768      2029
AOZ_R1.fastq    75343      1866
FIJ_R1.fastq      68518      1615