Off topic:Using Peas To Convert Hapmap To Plink Format

Question

[J.F.Jiang]

hello, everyone!

i am using the peas software for file format conversion test. The data i used is the data peas offered. I use 1.1HapMapDatatoStandard part first convert the hapmap data to standard mode, and then changed the suffix to inp while modify pops.inp for calculation.

when i get the ped and map(pedsnp original file) files, i use the plink software cmds:

plink --file 1pops(file name for ped and map) --r2 --noweb for LD calculation, but it turns out to be wrong: 

plink --file 1pops --r2 --noweb

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ]
Writing this text to log file [ plink.log ]
Analysis started: Tue May 31 21:10:52 2011

Options in effect:
        --file 1pops
        --r2
        --noweb

54881 (of 54881) markers to be included from [ 1pops.map ]

ERROR:
A problem with line 1 in [ 1pops.ped ]
Expecting 6 + 2 * 54881 = 109768 columns, but found 106612

i tried several times and checked the file, but i have not seen any problem yet. So could anybody here tell me which part goes wrong?

and why do the plink software need the formula to check the columns?