SLURM submission problem: Indexing the Reference Genome is not done in STAR

Question

[n_navy]

Hello, I tried to generate ref index using STAR with this code;

#!/bin/bash

/truba/home/user/STAR-2.7.7a/source/STAR --runThreadN 16
--runMode genomeGenerate
--genomeSAsparseD 2
--limitGenomeGenerateRAM 20000000000
--genomeDir /truba/home/user/index
--genomeFastaFiles /truba/home/user/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
--sjdbGTFfile /truba/home/user/Homo_sapiens.GRCh38.111.gtf
--genomeSAindexNbases 12_*

But it gave error;

*-bash-4.2$ ./generate_index.sh
Apr 17 10:17:17 ..... started STAR run
Apr 17 10:17:17 ... starting to generate Genome files
Apr 17 10:21:17 ..... processing annotations GTF
Apr 17 10:21:48 ... starting to sort Suffix Array. This may take a long time...
Apr 17 10:22:00 ... sorting Suffix Array chunks and saving them to disk...
./generate_index.sh: line 11: 73189 CPU time limit exceeded (core dumped) /truba/home/user/STAR-2.7.7a/source/STAR --runThreadN 16 --runMode genomeGenerate --genomeSAsparseD 2 --limitGenomeGenerateRAM 20000000000 --genomeDir /truba/home/user/index --genomeFastaFiles /truba/home/user/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --sjdbGTFfile /truba/home/user/Homo_sapiens.GRCh38.111.gtf --genomeSAindexNbases 12*

**And ref is not completed;**
*Log.out chrName.txt chrStart.txt exonInfo.tab sjdbList.fromGTF.out.tab
chrLength.txt chrNameLength.txt exonGeTrInfo.tab geneInfo.tab transcriptInfo.tab*

What should I do?

Thanks.

Answer 1

[Pierre Lindenbaum]

CPU time limit exceeded

your command is taking too long and can't be completed.

check your cluster documentation to allocate more time.

[n_navy]

I add these parameters;

#SBATCH -N 4
#SBATCH --tasks=1
#SBATCH -c 4
#SBATCH --time=24:00:00

But it keeps giving error

[Dave Carlson]

You're allocating 4 compute nodes (#SBATCH -N 4), but STAR can't actually make use of more than 1 compute node. You can increase the number of cores you're using on a single node, however ,by changing the value given to #SBATCH -c. 10 or 12 cores should be sufficient to build the index in a couple of hours or so, but be sure to check with your cluster documentation to determine what is allowed and what, if any, costs would be incurred.

[GenoMax]

But it keeps giving error

Please tell us what the error is.

[n_navy]

Error is; line 16: 75475 Killed or core dumped.

I increase the core but it did not work. Can you please write the parameters?