STAR mapping with genomeLoad issue bash script

Question

[luckysardar171]

Hello,

I am trying map RNA seq data in STAR bash script with the below command when I am running script its going in sleep mode

script which I am running

 date
STAR --genomeLoad LoadAndExit --genomeDir /media/index/
for f in `ls -1 *_1.fastq.gz | sed 's/_1.fastq.gz//' `
do
echo  ""${f}
STAR --readFilesIn ${f}_1.fastq.gz ${f}_2.fastq.gz\
     --outFileNamePrefix ${f}. \
     --readFilesCommand zcat \
     --runThreadN 8 --outSAMtype BAM \
     --genomeLoad LoadAndKeep \
     --genomeDir /media/index/ \
     --sjdbGTFfile /media/mm10.gtf

STAR --genomeLoad Remove --genomeDir /media/index/
done 
date

please help me to figure it out what is the mistake in the script

[Pierre Lindenbaum]

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