Illumina Genotyping in parallel raise an error
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nadne ▴ 10
@nadne-9806
Last seen 5.2 years ago

Hello,

I'm trying to genotype an Illumina SNP array. As I have many samples, I run it with the parallel options.

library(parallel)
library(doMC)                                                                                                                                                                                             
NUM_CORES = detectCores()
registerDoMC(NUM_CORES)                                                                                                                                                                                             
​library(crlmm)
options("krlmm.cores" = NUM_CORES)
g = genotype.Illumina(cdfName='humanomni25quadv1b', path=dir_path, call.method='krlmm', verbose=TRUE)

 

But I get the next error:

...
Processing sample stratum 49 of 50
Error in FUN(x, ...) : task 1 failed - "invalid 'n' argument"
Calls: genotype.Illumina ... preprocessInf -> ocLapply -> %dopar% -> <Anonymous>
Execution halted

What cause this error? How can I solve it?

crlmm snp illumina • 688 views
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