IndexError: list index out of range

[alimadani]

I used rose previously to call super-enhancers, however I cannot make rose2 work on the same files. I used bed files (ENCODE files) with all the columns or only the first 3 columns (chr, start, end) but it gives the same error all the time "IndexError: list index out of range".
I was wondering if you could help me figuring out the issue. It would be great if you can provide me first few lines of a bed or gff file that you have used previously to call super-enhancers with rose2. I appreciate your help!

Ali