genomeGenerate error

[Hiro]

Dear Allen

I  would like to perform mapping of RNA-seq reads to the large genome with 21 chromosomes (~15G bp) by STAR software.

I tried to use genomeGenerate command on Linux (RAM 128G) as follows.

STAR —runMode genomeGenerate —genomeDir usr —genomeFastaFiles WGA.fasta —limitGenomeGenerateRAM 100000000000

The genomeGenerate process started and  some SA files were generated.

But I got following error message and program stopped.

Jul 21 11:31:09 ... loading chunks from disk, packing SA...

terminate called after throwing an instance of 'std::bad_alloc'

  what():  std::bad_alloc

Stopped

I wonder if RAM is shortage for large genome. 

Could you help me with this problem. 

I’m looking forward to hearing of your answer.

Best wishes,

[Alexander Dobin]

Hi Hiro,

~15GigaBases genome would require ~128GB, probably just a bit above 128GB that you have,

If you send me the Log.out file, I can tell you exactly how much RAM it needs.

You can use the sparse array (--genomeSAsparseD 2) which will drop RAM requirement to ~70GB.

Cheers

Alex