Probably, you misunderstand what read merging is. There are two different types of merging (when you overlap reads by their ends, or when you just combine two files with reads into one), and none of them result in "merge_R1.fastq" and "merge_R2.fastq" files. Also, Spades does not require reads to be merged, whatever you mean by merging.

Bbmerge overlaps reads by their ends. You can use a command like:

bbmerge.sh in1=reads_R1.fastq in2=reads_R1.fastq out=merged.fastq outu1=unmerged_R1.fastq outu2=unmerged_R2.fastq ihist=ihist.txt