Total reads after trimming is the SAME as Initial number of reads

Infrastructure and utilities KneadData
1

Tool:
kneaddata v0.12.0

I notice that the total reads after trimming are the same as the initial number of reads. I am not sure what parameters would need to be adjusted or what may be causing this. Is this something to be concerned about?
The final number of reads (paired_1/2.fastq files) are different so I know that QC is being performed.

As an example,

  • Initial number of reads R1: 4038815.0
  • Total reads after trimming 1: 4038815.0
  • Toal reads paired_1: 3993709.0
for sample in `cat samples.txt`; do
kneaddata -i1 rawseqs_QCinput/$sample*R1* -i2 rawseqs_QCinput/$sample*R2* -o kneaddata --threads 10 --max-memory=1000m \
--reference-db /data/databases/human/ \
--trimmomatic=/data/Microbiome/RefData/Metagenomics/biobakery_workflows_databases/Trimmomatic-0.39/ \
--trimmomatic-options ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:TRUE \
--sequencer-source TruSeq3 \
--trf /home/fsaravia/.conda/pkgs/trf-4.09.1-hec16e2b_2/bin/
done