Hello, I have a question about STAR alignment with multiple files. I am using it from server and so my memory is limited (I have some restrictions unfortunately). So I have 12 files can I align them by grouping them as 6 to 6. In the first run; 6 of them and in the last run the other 6 of them. Does it create a problem for further processes such as quantification and diff gene exp analysis?

#!/bin/bash
#SBATCH -p hamsi
#SBATCH -A proj2
#SBATCH -c 28
#SBATCH -N 1
#SBATCH -t 0-4:00
#SBATCH -J star_alignment
#SBATCH -o star_alignment_%j.out
#SBATCH -e star_alignment_%j.err

cd ~/GSE121634_HCC4006

for file in $(cat ./acc_number.txt); 
do
~/STAR-2.7.10a/bin/Linux_x86_64_static/./STAR --runThreadN 28 \
--genomeDir ~/index/ \
--readFilesIn ./${file}_1.fastq.gz ./${file}_2.fastq.gz \
--readFilesCommand zcat \
--outFileNamePrefix ~/GSE121634_HCC4006/${file} \
--outSAMtype BAM SortedByCoordinate
done

It gives me a memory error then I tried without for loop.

#!/bin/bash
#SBATCH -p hamsi
#SBATCH -A proj2
#SBATCH -c 28
#SBATCH -N 1
#SBATCH -t 0-4:00
#SBATCH -J star_alignment
#SBATCH -o star_alignment_%j.out
#SBATCH -e star_alignment_%j.err

cd ~/GSE121634_HCC4006/Alignment

~/tools/STAR-2.7.10a/bin/Linux_x86_64_static/./STAR --runThreadN 28 \
--genomeDir ~/index/ \
--readFilesIn SRR8088215_1.fastq.gz,SRR8088216_1.fastq.gz,SRR8088217_1.fastq.gz,SRR8088218_1.fastq.gz,SRR8088219_1.fastq.gz,SRR8088220_1.fastq.gz,SRR8088221_1.fastq.gz,SRR8088222_1.fastq.gz,SRR8088223_1.fastq.gz,SRR8088224_1.fastq.gz,SRR8088225_1.fastq.gz,SRR8088226_1.fastq.gz,SRR8088227_1.fastq.gz,SRR8088228_1.fastq.gz,SRR8088229_1.fastq.gz,SRR8088230_1.fastq.gz,SRR8088231_1.fastq.gz,SRR8088232_1.fastq.gz SRR8088215_2.fastq.gz,SRR8088216_2.fastq.gz,SRR8088217_2.fastq.gz,SRR8088218_2.fastq.gz,SRR8088219_2.fastq.gz,SRR8088220_2.fastq.gz,SRR8088221_2.fastq.gz,SRR8088222_2.fastq.gz,SRR8088223_2.fastq.gz,SRR8088224_2.fastq.gz,SRR8088225_2.fastq.gz,SRR8088226_2.fastq.gz,SRR8088227_2.fastq.gz,SRR8088228_2.fastq.gz,SRR8088229_2.fastq.gz,SRR8088230_2.fastq.gz,SRR8088231_2.fastq.gz,SRR8088232_2.fastq.gz
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate

So will it create a problem by running them separately? Thanks in advance