When you have a list of input files that you want to analyze, but the software you are using doesn't support paralelization, a convenient way of speeding up the analysis is by running the program on a subsets of your files at the same time.
If you have a list of input files in one file (input.files.txt), it can easily be split into multiple files using the linux split command.
split -a 2 -l 500 -d input.files.txt input.file.
which will produce files named:
with each file containing 500 rows.