STAR genome generate taking long time and less thread.
1
0
Entering edit mode
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%.

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.

RNA-Seq STAR-Aligner Bioinformatics • 1.6k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
ADD REPLY
3
Entering edit mode
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).

ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1834 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6