#!/bin/bash
#$ -N bwa-mem2_indeksiranje
#$ -cwd
#$ -pe p28-mpisingle 2
#$ -l memory=40

module load bioinfo/bwa-mem2/2.2.1  

bwa-mem2 index human_g1k_v37.fasta

For indexing you need large amount of RAM memory. It is roughly 28 GB of RAM per GB of data. You need to use -l memory parameter to be sure you will have enough memory available. Use p20 and p28 ques as they have 120 GB of RAM memory available. Requested memory with -l memory parameter is per requested core ( in the example above the system will reserve 80 GB of RAM, 2 x 40GB). bwa-mem2 doesn't use more then one core. To get more memory for indexing do not increase core number but increase memory.

#!/bin/bash
#$ -N bwa-mem2
#$ -cwd
#$ -pe *mpisingle 16

module load bioinfo/bwa-mem2/2.2.1

bwa-mem2 mem -t $NSLOTS human_g1k_v37.fasta human_g1k_v37.fasta SRR7733443_1.fastq SRR7733443_2.fastq > d3_align.sam