On some OS the first grep produces results that are separated by a record separator line that is "-------------". Second grep removes those separators (there are commands in grep not to produce the separator but implementations of grep differ for various OS so I added second grep)
What happens on your machine if you just use the first part? Does it produce the record separators?
If grep is not producing clean Read 1/2 files then there may be some other formatting issue (wrapped lines, malformed/truncated fastq records etc) in your files.
What happens on your machine if you just use the first part? Does it produce the record separators?
Code:
$ grep -A 3 "_1:N" your_file | more
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