Error running smartpca from eigensoft: failed to create thread
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6 weeks ago
Jautis ▴ 410

Hello, I'm trying to run smartpca from the eigensoft package (v. 6.1.4). However, I get a premature termination with a "Failed to create thread" error. Any idea where this is coming from or how to fix it? I've attached below my command and the standard out. thanks in advance!

parameter file: pca_pars.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
genotypename: ../v44.3_HO_public.geno
snpname: ../v44.3_HO_public.snp
indivname: ../v44.3_HO_public.ind
evecoutname: MyProject.HO.merged.pca.evec.txt
evaloutname: MyProject.HO.merged.pca.eval.txt
poplistname: ./pca_populations.txt
lsqproject: YES
## smartpca version: 13050
norm used

lsqproject used
read 1073741824 bytes
read 1971990900 bytes
packed geno read OK
number of samples used: 1005 number of snps used: 593124
Using 55 threads, and partial sum lookup algorithm.
 snp        Affx-50012853 ignored . allelecnt:     0  missing:     0
 snp        Affx-50013327 ignored . allelecnt:     0  missing:     1
 snp        snp_1_1934796 ignored . allelecnt:     0  missing:    66
 snp          rs115998910 ignored . allelecnt:     0  missing:     3
 snp        Affx-50018835 ignored . allelecnt:     0  missing:     1
 snp        snp_1_2326032 ignored . allelecnt:     0  missing:     0
 snp        Affx-50025378 ignored . allelecnt:     0  missing:     2
 snp        snp_1_3257051 ignored . allelecnt:     0  missing:     0
 snp        snp_1_3661538 ignored . allelecnt:     0  missing:     1
 snp        snp_1_3799946 ignored . allelecnt:     0  missing:    64
fatalx:
Error: Failed to create thread.
Aborted
pca genotypes smartpca eigensoft • 243 views
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Thanks Pierre, I didn't see anywhere than the number of threads was a mandatory parameter.

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Resolved by Pierre's comment.

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