Hi,

I am trying to use BreaKmer to look for structural variants on Ion Ampliseq data. When I use the v0.0.6 version (and v.0.0.6.b), I get this message (sent stop message to server) when I try to run the soft :

[ahmed@ae ~]$ python /home/ahmed/Downloads/BreaKmer-Breakmer_0.0.6_Profile_CCGDProduction/breakmer.py /home/ahmed/Documents/references/breakmer_analysis.cfg
12/06/2017 02:33:33 PM - root - ERROR - Keep repeat regions option is false, but no repeat mask bed file provided. All repeat region variants will be reported.
sent stop message to server

I hope I use the right version of the soft, it looks very similar to the documentation in GitHub.

Would anyone have an idea ?

Thanks a lot for your precious help !

Best, Will