Dear All!

I want to make a smartpca PCA. I prune the background with the following code:

plink --bfile BACKGROUND_1  --maf 0.005 --make-bed --out BACKGROUND_1_HF >KINSHIP_AMR_MAF_log.txt

# pruning linked markers
plink --bfile BACKGROUND_1_HF  --indep-pairwise 200 5 0.3 > KINSHIP_AMR_PRUNE_log.txt
plink --bfile BACKGROUND_1_HF --extract plink.prune.in --make-bed --out BACKGROUND_1_done >>KINSHIP_AMR_PRUNE_log.txt
plink --bfile BACKGROUND_1_done --recode tab --out BACKGROUND_ALL

Then, using the same plink.prune.in file, I prune the samples:

plink --bfile SAMPLES  --maf 0.005 --make-bed --out SAMPLES_HF > KINSHIP_AMR_SAMPLES_MAF_log.txt
plink --bfile SAMPLES_HF --extract plink.prune.in --make-bed --out SAMPLES_done >KINSHIP_AMR_SAMPLES_PRUNE_log.txt
plink --bfile SAMPLES_done --recode tab --out SAMPLES_ALL

After this I want to merge the two datasets and merge it with CONVERTF's mergeit option using this par. file:

geno1: BACKGROUND_ALL.ped
snp1:  BACKGROUND_ALL.map
ind1:  BACKGROUND_ALL.ped
geno2: SAMPLES_ALL.ped
snp2:  SAMPLES_ALL.map
ind2:  SAMPLES_ALL.ped
genotypeoutname: ALL.geno
snpoutname:      ALL.snp
indivoutname:    ALL.ind
outputformat: EIGENSTRAT

But I always get fatalx: (getsnps) null snpnameAborted (core dumped) Error code. I tried that first i convert both datasets to EIGENSTRAT then to mergeit, get the same problem. How can I solve it?