Most programs do not allow you to use unpaired fastq files that remain after trimming along with properly paired files in the same alignment run. You will need to align the files with singleton reads individually.

bbwrap.sh from BBMap can do this:

BBWrap is a simple wrapper that allows BBMap to be run multiple times without reloading the index each time. So, it can save some compute resources (particularly with a small number of reads and large reference), and is also handy for things like mapping paired and unpaired reads to the same reference, then outputting them in the same file.