Error: Half-missing call in .ped file at variant 3, line 1.

[JUNXI FENG]

Hi,

I am new to plink, and when I tried to run association analysis, it gave me this error.

This is the first line of my tab separated file. The first six columns are added according to the requirement. 

Thanks!!

[Christopher Chang]

That's not a .ped file (see https://www.cog-genomics.org/plink/1.9/formats#ped for a short description).  If you used your own script to generate it, I strongly recommend targeting a different file format, such as VCF; .ped has been obsolete for close to a decade.