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