CONFIGURATION ERROR: Reference genome mismatch:

[HyojeenLee]

Hellp, I got an error like below.

CONFIGURATION ERROR:
Reference genome mismatch: Reference fasta file is missing a chromosome found in the normal BAM/CRAM file: 'chr11_KI270721v1_random'.

I used in aligning, an indexed version of reference genome (hg39.fa to) hg38.mmi (which was suggested by minimap2 to reduce time),
then should I use the same hg38.mmi or hg38.fa for the reference in Strelka configuration?

Thank you