<p>If you have worked on cluster with submitting jobs, please help me in resolving the following error.</p>
<p>I am running rsem pipeline to generate star index. In principal STAR requires more than 30G of RAM for human genome.</p>
<p>I have following script</p>
<pre><code>#!/bin/bash
#SBATCH --mail-user=&lt;your_email_address&gt;
#SBATCH --mail-type=end,fail
#SBATCH --job-name=&quot;job01&quot;
#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
 
</code></pre>
<p>The process fails as soon as it starts to generate genome files using star. Below is the error complaining about the memory.</p>
<p>I have put 5 threads for star usage and 10G for each cpu.</p>
<p>here is the error</p>
<pre><code>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
&quot;/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&quot; failed! Plase check if you provide correct parameters/options for the pipeline!
</code></pre>
<p>Could anyone of you tell me how to fix this.</p>
<p>Thank you</p>

CC BY-SA 4.0
2021-02-25T15:51:01.927Z
Have you tried allocating more than 10GB of RAM? It seems like the error is related to memory..
h3ab74
CC BY-SA 4.0
2021-02-25T16:09:26.060Z
I have tried till 50G. Don't know what is happening
Angelo
CC BY-SA 4.0
2021-02-26T03:08:43.313Z
Users have reported similar issues to STAR before: https://github.com/alexdobin/STAR/issues/129
Phoenix Mu
<star><rsem><slurm>
SLURM script for running RSEM star fails
# SLURM script for running RSEM star fails

(Asked by: username_0 on 2021-02-25)

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=
#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

**Tags:** star, rsem, slurm
> **Comments:**
> **username_1**: Have you tried allocating more than 10GB of RAM? It seems like the error is related to memory..  
> **username_0**: I have tried till 50G. Don't know what is happening  
> **username_2**: Users have reported similar issues to STAR before: https://github.com/alexdobin/STAR/issues/129  

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## 0 answers

