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


I have problem with genomeGenerate. I am using STAR_2.5.0c_modified. I started genomeGenerate as below.

$ STAR --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles platanus_k35_gapClosed.substituted.fixfasta.fasta --runThreadN 20 --limitGenomeGenerateRAM 64000000000

and got error.

Jan 18 23:17:24 ..... Started STAR run
Jan 18 23:17:24 ... Starting to generate Genome files
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

I attach my Log.out. Log.out.gz

Thank you for your kind helps!


About this issue

  • Original URL
  • State: closed
  • Created 8 years ago
  • Comments: 17 (6 by maintainers)

Most upvoted comments

Hi Takashi,

If you are using a genome with a large > 5,000 number of references (chrosomes/scaffolds), you may need to reduce the --{genomeChrBinNbits to reduce RAM consumption. The following scaling is recommended: --genomeChrBinNbits} = min(18, log2(GenomeLength/NumberOfReferences)). For example, for 3~gigaBase genome with 100,000 chromosomes/scaffolds, this is equal to 15.

Cheers Alex

Hi Chen,

for a fasta file: $ grep “^>” Genome.fasta | wc -l

Cheers Alex