Hi biostars people,

I am trying to run smartpca from eigensoft using the resultant plink file from population (STACKS).

When I try to run it, it gives out error claiming that:

warning (mapfile): bad chrom: 0    185735_10    0    631    T    C
warning (mapfile): bad chrom: 0    103794_12    0    647    C    A
warning (mapfile): bad chrom: 0    232483_35    0    867    T    C
warning (mapfile): bad chrom: 0    107649_23    0    928    T    C
warning (mapfile): bad chrom: 0    188043_10    0    1054    G    C
warning (mapfile): bad chrom: 0    250387_35    0    1098    T    C
warning (mapfile): bad chrom: 0    250793_7    0    1450    T    C
warning (mapfile): bad chrom: 0    356259_7    0    1578    A    G
warning (mapfile): bad chrom: 0    101214_32    0    1666    G    A
warning (mapfile): bad chrom: 0    421487_58    0    2057    A    C
genetic distance set from physical distance

I did some searching and changed my chromosome column.

Initially, my first few lines of map file looked like this:

#   Stacks   v1.34;   PLINK   v1.07;   December   14,   2015
scaffold100059_size1319    44_24    0    18480
scaffold100059_size1319    50_15    0    19964
scaffold100059_size1319    197153_14    0    39466
scaffold100059_size1319    197155_56    0    50909
scaffold100059_size1319    389671_9    0    54896

I have changed the chromosome to just numbers ranging lower than a thousand (from 1 to 117).

But it still gives the same error as before....

Now my first few lines look like this:

1    44_24    0    18480
1    50_15    0    19964
1    197153_14    0    39466
1    197155_56    0    50909
1    389671_9    0    54896

Can someone help me please?

Shane