How to make a genome assembly file with two scaffold files?

Question

[ongchip]

I have two scaffold files from one sample. I want to make genome assembly file with them. There is also the reference genome of the relative species in the same genus. Which program is suitable?? I could't use the RagTag. There was the error: [Errno 13] Permission denied: 'ragtag_correct.py'. I am a root user so that please let me know the program without the permission.