Problem filtering fastq files with PRINSEQ

[sh82...@gmail.com]

Hi there,
I am using PRINSEQ for filtering my paired end illumina fastq files based on quality score, using the command:

perl prinseq-lite.pl -fastq MS-1_1.fastq -fastq2 MS-1_2.fastq -min_qual_score 30

In result, I get both 'good', and 'bad' files.

Now the problem is this: when I assess the quality of these 'good files' with another tool "FastQC tool", it shows that QC of 'good file' fails, because these good files contain reads with quality score below 30. I would upload graphs to clear it further, but perhaps image uploading is not provided.

Please suggest is there any problem with the command I used. Thanks