Reading PLINK FAM file from [adm8.fam]. 3000 individuals to be included from [adm8.fam]. Reading PLINK BIM file from [adm8.bim]. 994596 SNPs to be included from [adm8.bim]. Warning: Duplicated SNP ID "M_994595" has been changed to "M_994595_994596" .Reading PLINK BED file from [adm8.bed] in SNP-major format ... Genotype data for 3000 individuals and 994596 SNPs to be included from [adm8.bed].
The analysis run, but only for 994596 SNPs instead of the 1727769 intended.
The BED file used does not seem to have any issue, I don't see any duplicate SNPs, and plink reports the correct number of SNPs with the same BED file:
wc -l plink.snplist 1727769 plink.snplist
Any idea what could be wrong? Many thanks in advance