STAR genome generate taking long time and less thread.

Question

[Ranan Jyoti Sarma]

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%.

https://drive.google.com/open?id=1Tp8ZzEkE0fha6pl0iPnfBcnjK9PpT1Av "Screenshot of command running

https://drive.google.com/open?id=1QRUCGvhOxef9Hm5FCRfdHpbXwm6cuL1q "Screenshot of thread utilization"

I would appreciate your suggestions.

[Susmita Mandal]

How big is the genome file? Exactly how much time STAR is taking? And what is the spec of your computer system?

[Ranan Jyoti Sarma]

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

[WouterDeCoster]

How to add images to a Biostars post

Answer 1

[Nicolas Rosewick]

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).

[Ranan Jyoti Sarma]

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 .