This is a test version of Biostars. For the public version, visit https://www.biostars.org.
STAR genome generate taking long time and less thread.

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.

rna-seq star
• 4,297 views • link
updated by Ram Ram • written by Ranan Jyoti Sarma Ranan Jyoti Sarma

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

• 0 views • link
written by Susmita Mandal Susmita Mandal

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

• 0 views • link
written by Ranan Jyoti Sarma Ranan Jyoti Sarma

1 answer

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).

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

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 .

• 0 views • link
written by Ranan Jyoti Sarma Ranan Jyoti Sarma

Log in to answer this question.

More posts like this