Bowtie2 alignment error with different amount of reads in R1 and R2

Hi all,
I have an issue when trying to align a ChIPseq input reads to the genome using bowtie2. The error that comes up is:
Error, fewer reads in file specified with -2 Error, fewer reads in file specified with -2 than in file specified with -1than in file specified with -1

I have removed singletons using fastq_pair but it still seems as though R1 and R2 have different amount of reads… What could be the cause of this and how do I fix it?