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Can I use BAM files where RNA-Seq reads have been mapped to the genome rather than the transcriptome?

I'm running this command on Ubuntu 20.04 (WSL) and getting the error below. The FASTA file is a standard human reference that was used successfully to make a STAR and Bowtie2 references. Any suggestions?

root@FBS0255AGAM:~/d/test/emsar# emsar-build --PE -p 8 hg_GRCh38_p13_v106_202202.fa 20-69 rsh human
Paired-end= y
strand type= ns
Max_Fraglen= 400
Min_Fraglen= 1
MAX_REPEAT= 100
bias model= 0 (no bias model)
positional bias training length= 1000
positional bias impute training length= 200
fasta header option= E
MAX_Thread= 8
binsize = 5000
taglen = 2
print suffix aray = n
finished reading options and arguments..
input fastafile name= hg_GRCh38_p13_v106_202202.fa
readlength = 20
reading fasta file... :04/04,17:20:27
initialized seq_array..
Segmentation fault