Hotspot error during run_pass2_hotspot and during run_10kb_counts

Question

[scambier]

Hello-

I'm trying to run hostpot, and am getting the following error when using the test data and files provided:

run_pass2_hotspot: processing /home/ubuntu/hotspot/data/test_DNase_seq.hg19-pass2
generating 50kb pad set...
May use bedops --help for more help.

Error: Error: stat() failed on: stdin

When I try to process my own data, hotspot just quits during the run_10kb_counts script, (no error message).

I'm a beginner to linux/command line/next-gen analysis, so it's quite possible I've made some very basic/silly errors. I have very closely followed the directions provided in the readme file, and am (fairly) certain I have all the required dependencies and have made the proper changes to the runhotspot and runall.tokens.txt files.

Any help or guidance would be greatly appreciated.