Can I stop my nanopore sequencing run if there are no more reads being produced? I am sequencing a whole genome on MinION. I have used this flow cell for 6 hours for the phage lambda control. That gave me around 300,000 reads. I started a 48h sequencing run on the same flow cell after washing it. The sequencing has been going on for 1 day and 21 hours. It is not producing any reads at the moment (Strand = 0). The number of single pores is also 0. Can I "Stop acquisition" without negatively affecting the results?

The image below is a screenshot taken from MinKNOW, the software used to control the MinION.
Yes, you can click "stop acquisition" and your run won't be negatively affected. All of the reads are saved as they are generated. I am not sure how this will impact live basecalling though if that is something that you do.