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STAR indexing gets killed on its own at a particular time (while generating suffix arrays)

I used the following command to build STAR index:

/path/to/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /path/to/star_index
--genomeFastaFiles /path/to/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /path/to/Homo_sapiens.GRCh38.86.gtf

The process gets "killed" after a certain point of time. I am running the process on 32G RAM, 1TB HDD, and 4 cores and STAR version 2.6. What could be the issue, memory allocation or STAR version?

rna-seq software error next-gen sequencing
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updated by caggtaagtat caggtaagtat • written by shuksi1984 • shuksi1984

1 answer

I think STAR uses a lot of RAM (~30GB), so that could be an issue. You can reduce the RAM requirements with the "sparse" mode, this will make it a little slower thou.

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written by caggtaagtat caggtaagtat

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