Alignment does not end

[kendaida]

Hi thank you for developing this cool tool!
I am running ~50 samples at the same time, most of them finished in a few hours but some of them were alining the reads even after three days.
Some of the long taking samples finished the run after three days.

I am using paired end read fastq, the size is about 3~5Gb for each file.
Happy to have any suggestions to solve this situation.