STAR indexing

[Shuksi]

When I used following command, several SA index files are generated.

/path/to/star/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /path/to/star/genome_file --genomeFastaFiles /path/to/GCF_000001405.31_GRCh38.p5_genomic.fna --sjdbGTFfile /path/to/human.refseq.gtf --sjdbOverhang 100 --limitGenomeGenerateRAM=8825541333

Also, it is taking several hours.

File size are accordingly:
human.refseq.gtf-227MB
genomic.fna-3.1GB
STAR version-STAR-2.5.3a

I am running on 16GB RAM and ~400GB HDD

I am getting following message on terminal:
Apr 09 11:53:04 ..... started STAR run
Apr 09 11:53:04 ... starting to generate Genome files
Apr 09 11:53:47 ... starting to sort Suffix Array. This may take a long time...
Apr 09 11:53:59 ... sorting Suffix Array chunks and saving them to disk...

I have attached log.out file.

[Alexander Dobin]

Hi Shuksi,

16GB is not enough for human genome with deafult parameters, you would need ~32GB.

If you want to try to fit the genome into 16GB, you would need:

--genomeSAsparseD 2 --genomeSAindexNbases 12 --limitGenomeGenerateRAM 15000000000

Cheers

Alex

[Shuksi]

Hi Alex,

Thank you for your response. I used:

path/to/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir path/to/genome_file --genomeFastaFiles path/to/genomic.primary_assembly.fna --sjdbGTFfile /path/to/human.gtf --sjdbOverhang 100 --limitGenomeGenerateRAM=8825541333 --genomeSAsparseD 2

And, it worked.

Shuksi