MCL Clustering for Large BLAST output files

Hello,

I have pairwise blast result for more than 400 bacterial genome each genome has more than 5000 sequences. I want to cluster the similarity information using MCL to identify protein families. However, when Im trying to run MCL clustering program on the output file. MCL is running out of memory even on machine with 24 GB RAM. The total size of BLAST output file is more than 300 GB after parsing out only best reciprocal hits. Can any one suggest me a way to perform this operation in better way?

Thank you