Getting error at the clumping stage of PRSice 2

Question

[m.shoaib]

Hi,

I using PRSice 2 and getting error at the clumping stage, total variants included by PRSice are 4517408

Rscript PRSice.R\
    --prsice PRSice_linux\
    --dir /home/shoaib/projects/base-files/T2test/PRSice\
    --base T2baseNoBMI.txt\
    --target T2basePRS#\
    --snp rsID\
    --chr CHR\
    --bp BP\
    --A2 A2\
    --A1 A1\
    --stat BETA\
    --binary-target T\
    --pvalue Pvalue\
    --pheno pheno-cas-cont.txt\
    --extract PRSice.valid\
    --no-clump\
    --out PRSice-res\

ERROR

Start performing clumping
std::bad_alloc
Begin plotting
Current Rscript version = 2.3.3
Error in fread(paste0(argv$out, ".summary"), data.table = F) :
  File 'PRSice.summary' does not exist or is non-readable.

when I am using --no-clump, it's working alright

Please suggest how to avoid error

Thanks

Answer 1

[Sam]

Not enough memory. This is something I am trying to solve at the moment. Using single thread can sometime solve the problem. If not, I will have to generate a copy where it uses a less aggressive algorithm for memory storage.

[m.shoaib]

I am reserving two cores for the analysis

#SBATCH --ntasks=2
#SBATCH --mem-per-cpu=500M

You think, reserving large memory would probably solve the issue?

[Sam]

Definitely. 500M x 2 is just 1G. That isn't enough even for genotyped data with 500k SNPs. You will need almost 100G for this.