I am running STAR for aligning wheat RNA-Seq data with Ensemble reference file . The size of reference file is 4gb. The genome directory created in the first step is 42 gb. The mapping step took more than 50 hours. Some jobs are still running for more than 75 hours
I used 5 nodes with 100gb each in our university cluster . Here is the script I used
I ran BWA-MEM on same data and it took less than 10 hours to complete the mapping. Am I doing something wrong or do I need to choose some other parameters ?
I used 5 nodes with 100gb each in our university cluster . Here is the script I used
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#!/bin/sh #SBATCH --job-name=STAR #SBATCH --nodes=5 #SBATCH --ntasks-per-node=1 #SBATCH --time=120:00:00 #SBATCH --mem=100g #SBATCH --error=<Error File Name> #SBATCH --output=<Output File Name> cd /Dir_PATH/STAR ./STAR_2.4.0b/STAR --genomeDir /Dir_PATH/STAR/index --readFilesIn /File_PATH/L001_R1_001.fastq,/File_PATH/L002_R1_001.fastq File_PATH/L001_R2_001.fastq,/File_PATH/_L002_R2_001.fastq --outFileNamePrefix /Dir_PATH/<Prefix_Name>/ --runThreadN 10
I ran BWA-MEM on same data and it took less than 10 hours to complete the mapping. Am I doing something wrong or do I need to choose some other parameters ?
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