Step	Problem	Possible Reason	Solution
7	There are no present calls (1 values) in the binarized data	Peak calls were provided opposed to aligned reads and the ‘-peaks’ flag was not specified	Use aligned reads or add the ‘-peaks’ option
10	Error message that the Information initialization strategy can only support a certain number of states	The binarization might not have been done correctly and there are no present calls. Alternatively more states are being asked for than there are observed combination of marks	If there are no present calls see troubleshooting for step 7. If there are more states than combination of marks either reduce the number of states or instead use the Random initialization strategy
10	Error message indicating insufficient memory	Java does not have access to enough memory or there is insufficient memory available on the system	Increase the memory Java has access to by increasing the value associated with the ‘-mx’ flag. Alternatively if using the ‘-p’ flag set it to a small non-zero integer value to reduce the number of processors and thus memory used simultaneously at a cost of additional runtime.