DIRECT.REPEAT.FINDER1: command not found and bwa-mem2 replace bwa mem

[ZHONGHONGXIN]

Hi, Circle_finder term,
l have a question is about Circle_finder/circle_finder-pipeline-bwa-mem-samblaster.sh #Step 1: Mapping.
bwa mem -t $1 $2 $3 $4 | samblaster -e --minNonOverlap $5 -d $6-$7.disc.sam -s $6-$7.split.sam -u $6-$7.unmap.sam > $6-$7.sam
But this step spend so long time, l want to use bwa-mem2 replace bwa mem, but l don't know how to build the bwa-mem2 index, whether or not copy this command: ./bwa-mem2 index [-p prefix] <in.fasta>? Please give me some useful advice.

And another question is about Circle_finder/microDNA.InOne.sh, the error information is as follows:
Circle_finder/Direct-repeat.withJT.sh: line 19: DIRECT.REPEAT.FINDER1: command not found! l don‘t know how to debug.

Thanks!
HongXin