STAR genome generate taking long time and less thread.
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2.9 years ago

Hi RNA-Seq/Bioinformatics community. My problem is with STAR tool. STAR genome generate is taking a lot of time for genome generating. My command is :

STAR --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles ref_genome.fa --sjdbGTFfile ref_annot.gtf --sjdbOverhang 75 -runThreadN 16


It is showing the utilization of only one thread to 100%.

RNA-Seq STAR-Aligner Bioinformatics • 1.6k views
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How big is the genome file? Exactly how much time STAR is taking? And what is the spec of your computer system?

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It is solved now. It was a small mistake as pointed by Nicolas Rosewick below.

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2.9 years ago

You made a mistake in your command by specifying -runThreadN 16 instead of --runThreadN 16. So that's why you have only on CPU working on it now. Kill the command and execute it again with the correct parameter. Also be sure to have enough RAM (FYI human genome takes ~40GB of RAM to run).

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Thanks... It's is resolved now. It was just a small mistake. 32 GB RAM with 32 GB SWAP memory. Around 15 GB of SWAP get utilized after full utilization of the main RAM .