How to change genome and make sure the number of HP_RCOUNT

[24efh]

Hi:
I am lin, a CHINESE graduate student who just wanna find some provocative suggestions from this forum. So fortunate for me to glimpse MitoHPC,which can meet my needs in 100 per cent ,but there are something hanppens following the first time i run all of codes with different consequences from different examples, i was deeply confused about this problem. I was wondering if you can give me some insightful advice. Here just the certain discription:
Runing example4 under the guidance of init.mm39.sh and generate this list of consequence：

Runing example2 under the guidance of init.sh and generate this list of consequence：

Both of the file name of twice running consequences are equal with each other,but vcf.file contents here are different from different examples. There are no consequences exist in any kind of vcf.file generated from examples1 with init.sh running in the first and second iteration, mutect2.mutect2.[3,5,10].tab.file are also in the same situation,except for mutect2 or mutect2.mutect2.00.concat.vcf from examples1. Runing examples4 with init.mm39.sh can generate normal files in my expectation.
Finally, i was a little confused about HP_FRULE,the number of HP_RCOUNT=61 and HP_RNAME,why i need to change things you've mentioned in README,becaues i want to detect the mitochrondrial hetroplasmy among fishs for different ages. how can i do to change my target Silver.Crap genome and get my ideal consequences that related with age .
Having long looked to your check and reply.