Question: STAR genome generate taking long time and less thread.
0
gravatar for Ranan Jyoti Sarma
11 weeks ago by
Mizoram Univesity
Ranan Jyoti Sarma40 wrote:

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 appriciate your suggestions.

ADD COMMENTlink modified 11 weeks ago by Nicolas Rosewick8.3k • written 11 weeks ago by Ranan Jyoti Sarma40

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

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Susmita Mandal50

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

ADD REPLYlink written 11 weeks ago by Ranan Jyoti Sarma40

How to add images to a Biostars post

ADD REPLYlink written 11 weeks ago by WouterDeCoster41k
3
gravatar for Nicolas Rosewick
11 weeks ago by
Belgium, Brussels
Nicolas Rosewick8.3k wrote:

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).

ADD COMMENTlink written 11 weeks ago by Nicolas Rosewick8.3k

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 .

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Ranan Jyoti Sarma40
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