The issue that I have Illumina mate pairs sequence, I filtered them using skewer it results in two fastq files forward and reverse.

There are some sequences that was removed from one of the files "did not pass the filtering process"

when I use bowtie2 it gives this error:

Error, fewer reads in file specified with -1 than in file specified with -2
terminate called after throwing an instance of 'int'
bowtie2-align died with signal 6 (ABRT)

Is there any script or software to exclude those sequences from the two files or I need to write my own?