Inconsistent Primer Removal in Different Amplicon Datasets Using Same cutadapt Command

[Rubadevis]

I am using cutadapt for trimming amplicon sequencing datasets generated in the same sequencing run, containing two different markers (16SAnimal and CO1), sequenced on the same flowcell. The trimming command and settings are identical for both datasets.

However, I observe the following differences:

For the 16SAnimal marker data, cutadapt removes adapters and primers, trying to retain the reads by not removing the partial matches

For the CO1 marker data, cutadapt remove maximum of the reads and retains a small portion of the raw reads, with reducing the data size significantly (from 16 GB to ~300 MB)

My question is why does cutadapt perform well on the 16SAnimal data but remove maximum of the reads in the CO1 data, using the exact same command?

Additional Informations:

adapter_file_co1.txt

adapter_file_16sA.txt

command used :

cutadapt -j 4 -a file:$adapter_file -A file:$adapter_file -q 20,20 --minimum-length 100 --poly-a -n 1 --nextseq-trim=20 -o "$TRIM_R1" -p "$TRIM_R2" "$R1" "$R2" >> "$LOGFILE" 2>&1

I would appreciate any guidance on improving the trimming process in CO1 data with cutadapt or suggestions if other tools are better suited for this.

Thank you!