Yes that might help me , Thank you very much for the help.

I am using the files hosted by Ensembl Data Base, and using the hisat2 version 2.1.0 to build the index. Following is the SLURM script which I use to build it. I will post it, where the memory, partition and qos might change depending on the cluster and the the scheduler which is been used.

#!/bin/bash
#SBATCH --job-name=hisat
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c 16
#SBATCH --mem=220G
#SBATCH --partition=general
#SBATCH --qos=general
#SBATCH -o %x_%j.out
#SBATCH -e %x_%j.err

#genome 
wget ftp://ftp.ensembl.org/pub/current_fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz
#GTF 
wget ftp://ftp.ensembl.org/pub/current_gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.94.gtf.gz


for file in *.gz; do
       gunzip -d $file
done
echo "=========== Unzip Done ================="

BASE_NAME="Rattus_norvegicus"
FASTA_File="Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa"
GTF="Rattus_norvegicus.Rnor_6.0.94.gtf"
SPLICE="splice_site"
EXON="exon"

module load hisat2/2.1.0
#create splice sites
hisat2_extract_splice_sites.py ${GTF} > ${SPLICE}

#create exone file
hisat2_extract_exons.py ${GTF} > ${EXON}

#build index
hisat2-build -p 16 --exon ${EXON} --ss ${SPLICE} ${FASTA_File} ${BASE_NAME}

#build large index if the above does not work
#hisat2-build -p 16 --large-index --exon ${EXON} --ss ${SPLICE} ${FASTA_File} ${BASE_NAME}

If the normal hisat2 build does not work, you can also try to build the large index using the commented part as well.

Thanks again for the help.