Question: STAR indexing gets killed on its own at a particular time (while generating suffix arrays)
1
gravatar for shuksi1984
2.1 years ago by
shuksi198460
shuksi198460 wrote:

I used the following command to build STAR index:

/path/to/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /path/to/star_index
--genomeFastaFiles /path/to/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /path/to/Homo_sapiens.GRCh38.86.gtf

The process gets "killed" after a certain point of time. I am running the process on 32G RAM, 1TB HDD, and 4 cores and STAR version 2.6. What could be the issue, memory allocation or STAR version?

ADD COMMENTlink modified 2.1 years ago by caggtaagtat1.3k • written 2.1 years ago by shuksi198460
1
gravatar for caggtaagtat
2.1 years ago by
caggtaagtat1.3k
caggtaagtat1.3k wrote:

I think STAR uses a lot of RAM (~30GB), so that could be an issue. You can reduce the RAM requirements with the "sparse" mode, this will make it a little slower thou.

ADD COMMENTlink written 2.1 years ago by caggtaagtat1.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1970 users visited in the last hour