Hello All! I am trying to map the RNA seq data with the reference genome using STAR aligner tool in cluster. I used the reference fasta file and gtf file to create the genomeDirectory that has the genome index. Now, I want to map the RNA seq data using that star index, however I get the following error:

**EXITING: FATAL INPUT ERROR: empty value for parameter "genomeDir" in input "Command-Line"
SOLUTION: use non-empty value for this parameter.****

Could you please help me with this? Here is the batch script that I ran to do the mapping. genom_dir which is star_index is the directory that has all the files created from the star index step.

#!/bin/bash
#

# job standard output will go to the file slurm-%j.out (where %j is the job ID)

#SBATCH --time=3:00:00   # walltime limit (HH:MM:SS)
#SBATCH --nodes=1   # number of nodes
#SBATCH --ntasks-per-node=16   # 16 processor core(s) per node
#SBATCH --mem=100G   # maximum memory per node
#SBATCH --mail-user=username@college.edu   # email address
#SBATCH --mail-type=END
#SBATCH --output=/output_directoy_path/map_out/"s-%j-0716_temp_map.out" # job standard output file (%j replaced by job id)

# LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE

# Load modules
#=====================================================#

#--| STAR
module load star/2.7.6a-wq7xoea


#=====================================================#
# Assign varialbles
#=====================================================#

#--| PATH
pKS="/working directory path/directory_name"

genom_dir= ${pKS}/"star_index"
inputFile = ${pKS}/"job"

#--| FILE
finput=${inputFile}/"temp.fasta"

#=====================================================#
# Run
#=====================================================#
#--| Make Mapping

STAR \
--runThreadN 8 --runMode genomeGenerate \
--genomeDir ${genom_dir}  \
--readFilesIn ${finput} \
--quantMode GeneCounts \
--outFilterMismatchNmax 0

~

genom_dir= ${pKS}/"star_index" should read genom_dir="${pKS}/star_index" (n.b., no space after the =); inputFile and finput also need to be changed accordingly.