Hello,
I'm new to this forum so forgive me if this post isn't the way it should be.
Im trying to run smartpca but am getting the following error:
smartpca -p smartpca_2.par
parameter file: smartpca_2.par
\### THE INPUT PARAMETERS
\##PARAMETER NAME: VALUE
genotypename: example.eigenstratgeno
snpname: example.snp
indivname: example.ind
evecoutname: eigenstrat_outlier_removed.evec
evaloutname: eigenstrat_outlier_removed.eval
outlieroutname: eigenstrat_outlier_removed.txt
numoutlieriter: 5
numoutlierevec: 10
outliersigmathresh: 6
usenorm: YES
familynames: NO
\## smartpca version: 13050
norm used
number of samples used: 88733 number of snps used: 4057
fatalx:
Unable to allocate 7873545289 unit(s) for item
Aborted (core dumped)
Could anyone tell me why this is happening ? I tried using the ped-map files and also tried after converting ped-map to eigenstrat format but the error remains the same. I even tried running it on a compute cluster.
Thanks a lot.
Please use the formatting bar (especially the
code
option) to present your post better.It's funny because max_virtual_mem on Sun Grid Engine shows 1G for ~ 90k samples and breaks while for 5k,10k the max_virtual_mem is 1.5, 3G and it runs to completion. When I raise to ~17k samples, it crashes again.
I'm trying flashpca2 instead since I dont know how to get smartpca to work on this large cohort size.
And it's a bus error (exit 137) for 17k and 20k while it's an allocation error for ~90k samples which also seems weird.
Please use the
ADD COMMENT
button to address Jean-Karim Heriche directly, instead of adding an answer. Could you correct this issue?