Parallelization of scan1snps (Error: k_loco not found)

[Senthil Thillainadesan]

Hello Karl,

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

I'm not sure if others have also experienced something similar or whether it is something I am doing.

Thanks

Senthil

[Karl Broman]

Can you show the code you used in both cases? It’s hard to see how this problem

might occur.

karl

On Aug 12, 2020, at 1:08 AM, Senthil Thillainadesan wrote:



[kidd...@gmail.com]

Sorry! I should have included the code to begin with.

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)