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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