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SLURM script for running RSEM star fails

Bioinformatics Asked by Angelo on April 24, 2021

If you have worked on cluster with submitting jobs, please help me in resolving the following error.

I am running rsem pipeline to generate star index. In principal STAR requires more than 30G of RAM for human genome.

I have following script

#!/bin/bash
#SBATCH --mail-user=<your_email_address>
#SBATCH --mail-type=end,fail
#SBATCH --job-name="job01"
#SBATCH --mem-per-cpu=10G

rsem-prepare-reference --gtf ~/Genomes/Homo_sapiens.GRCh38.100.chr.gtf -p 5 --star --star-path ~/Tools/STAR/bin/Linux_x86_64/ ~/Genomes/Homo_sapiens.GRCh38.dna.toplevel.fa ~/Genomes/GRCh38_100
 

The process fails as soon as it starts to generate genome files using star. Below is the error complaining about the memory.

I have put 5 threads for star usage and 10G for each cpu.

here is the error

rsem-preref /storage/homefs/as21u994/Genomes/GRCh38_100.transcripts.fa 1 /storage/homefs/as21u994/Genomes/GRCh38_100
Refs.makeRefs finished!
Refs.saveRefs finished!
/storage/homefs/as21u994/Genomes/GRCh38_100.idx.fa is generated!
/storage/homefs/as21u994/Genomes/GRCh38_100.n2g.idx.fa is generated!

/storage/homefs/as21u994/Tools/STAR/bin/Linux_x86_64//STAR  --runThreadN 8  --runMode genomeGenerate  --genomeDir /storage/homefs/as21u994/Genomes  --genomeFastaFiles /storage/homefs/as21u994/Genomes/Homo_sapiens.GRCh38.dna.toplevel.fa  --sjdbGTFfile /storage/homefs/as21u994/Genomes/Homo_sapiens.GRCh38.100.chr.gtf  --sjdbOverhang 100  --outFileNamePrefix /storage/homefs/as21u994/Genomes/GRCh38_100
Feb 25 12:10:58 ..... started STAR run
Feb 25 12:10:58 ... starting to generate Genome files

EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=31000000000is too small for your genome
SOLUTION: please specify --limitGenomeGenerateRAM not less than 168632691637 and make that much RAM available

Feb 25 12:18:11 ...... FATAL ERROR, exiting
"/storage/homefs/as21u994/Tools/STAR/bin/Linux_x86_64//STAR  --runThreadN 8  --runMode genomeGenerate  --genomeDir /storage/homefs/as21u994/Genomes  --genomeFastaFiles /storage/homefs/as21u994/Genomes/Homo_sapiens.GRCh38.dna.toplevel.fa  --sjdbGTFfile /storage/homefs/as21u994/Genomes/Homo_sapiens.GRCh38.100.chr.gtf  --sjdbOverhang 100  --outFileNamePrefix /storage/homefs/as21u994/Genomes/GRCh38_100" failed! Plase check if you provide correct parameters/options for the pipeline!

Could anyone of you tell me how to fix this.

Thank you

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