msisensor scan -d hg19.fa -o hg19msi 
msisensor msi -d hg19msi -n Bl_001_C_B.hg19.HQ.alignment.bam -t Bl_001_C_T.hg19.HQ.alignment.bam -o 001 Start at:  Thu Dec  5 17:53:04 2019

loading homopolymer and microsatellite sites ...

Total loading windows:  5885 

Total loading homopolymer and microsatellites:  1799277 

window: 0 done...:chr1:25453-525648
window: 1 done...:chr1:526113-1026672
window: 2 done...:chr1:1027417-1529226
...
window: 5740 done...:chr21:43511503-44012887
window: 5741 done...:chr21:44013397-44514110
window: 5742 done...:chr21:44513503-45010722
window: 5743 done...:chr21:45013564-45514344
window: 5744 done...:chr21:45514110-46015712
window: 5745 done...:chr21:46014153-46513813
window: 5746 done...:chr21:46516352-47018338
window: 5747 done...:chr21:47018835-47520803
window: 5748 done...:chr21:47519224-48020693
window: 5749 done...:chr21:48030412-48118446
Program aborted: 
Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!
The program created only empty files for somatic and msi scores but created germline and dist files. 
I am getting the same error for hg38,Tried all options couldn't get any output.