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Multi-core in scan1snps gives error about k_loco #177
Description
A user reported a problem with multi-core analysis with scan1snps(), where a kinship matrix wasn't found:
I've noticed when I run scan1snps with core set to greater than 1 I get an error that my kinship file ("k_loco" is not found). It works without a problem with cores=1
2 nodes produced errors; first error: object 'k_loco' not found
This works fine (using 1 core to do whole genome snp scan):
out_snps <- scan1snps(apr, map, phenol[,81], k_loco, Xcovar = NULL,addcovar = covars, query_func=query_variants, cores =1)
But if I change the cores argument to 2:
out_snps <- scan1snps(apr, map, phenol[,81], k_loco, Xcovar = NULL,addcovar = covars, query_func=query_variants , cores =2)
Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: object 'k_loco' not found
Interestingly if I run scan1snps on just an interval of interest there is no problem with using more than 1 core:
start=32.40
end=32.78
chr<-17
covars<-NULL
out_snps <- scan1snps(apr[,chr], map, phenol[,81], k_loco[[chr]], Xcovar = NULL,addcovar = covars, query_func=query_variants, chr=chr, start=start, end=end, keep_all_snps=TRUE, cores = 2)
Activity
kbroman commentedon Oct 12, 2020
I'm not able to reproduce this problem.
kbroman commentedon May 12, 2022
A similar problem was reported again. See this post on the R/qtl2 google group.
kbroman commentedon Jul 20, 2022
Another instance of this on the discussions group.