console.gwa.txt

> # Run GWAS analysis
> # Note: This function writes a file, but does not produce an R object
> start <- Sys.time()
> GWAA(genodata=genotype, phenodata=phenoSub, filename=gwaa.fname)
656890  SNPs included in analysis.
1309 samples included in analysis.
socket cluster with 2 nodes on host ‘localhost’
GWAS SNPs 1-65689 (10% finished)
GWAS SNPs 65690-131378 (20% finished)
GWAS SNPs 131379-197067 (30% finished)
GWAS SNPs 197068-262756 (40% finished)
GWAS SNPs 262757-328445 (50% finished)
GWAS SNPs 328446-394134 (60% finished)
GWAS SNPs 394135-459823 (70% finished)
GWAS SNPs 459824-525512 (80% finished)
GWAS SNPs 525513-591201 (90% finished)
GWAS SNPs 591202-656890 (100% finished)
[1] "Done."
Warning messages:
1: In GWAA(genodata = genotype, phenodata = phenoSub, filename = gwaa.fname) :
  Number of samples mismatch. Using subset found in phenodata.
2: closing unused connection 4 (<-localhost:11080) 
3: closing unused connection 3 (<-localhost:11080) 
> end <- Sys.time()
> print(end-start)
Time difference of 1.433755 hours
> save(genotype, genoBim, clinical, pcs, imputed, target, rules, phenoSub, support, file=working.data.fname(7))