[adegenet-forum] unable to import a diploid dataset using read.strucutre

Mon Dec 30 04:09:42 CET 2013

Dear

      I am unable to import a diploid dataset using read.strucutre.  I always got an error:

Converting data from a STRUCTURE .stru file to a genind object...

df2genind(X = X, pop = pop, missing = missing, ploidy = 2) :

  2 alleles cannot be coded by a total of 3 characters

I paste data (104 individual, 14 loci), Can you help fix this?

RADid_0000113 RADid_0000114 RADid_0000250 RADid_0000388 RADid_0000798 RADid_0001205 RADid_0001522 RADid_0001584 RADid_0001771 RADid_0002962 RADid_0003463 RADid_0003558 RADid_0004239 RADid_0004366

QCS10 1 0 2 2 -9 -9 -9 -9 -9 -9 2 2 2 2 1 1 -9 -9 1 2 1 2 1 1 1 1 1 1 1 1

QCS13 1 0 2 2 -9 -9 2 2 -9 -9 -9 -9 2 2 -9 -9 1 1 2 2 1 1 1 3 3 3 1 1 1 1

QCS16 1 0 2 2 -9 -9 -9 -9 1 1 2 2 2 2 -9 -9 1 1 2 2 1 1 1 1 1 3 1 1 1 1

QCS19 1 0 -9 -9 2 8 2 2 1 1 2 2 2 2 1 1 1 1 2 2 -9 -9 1 1 -9 -9 1 1 1 1

QCS22 1 0 -9 -9 2 2 2 2 1 1 2 2 -9 -9 -9 -9 1 1 2 2 1 1 3 3 1 3 1 1 1 1

QCS4 1 0 2 2 1 1 2 2 -9 -9 2 2 1 2 1 1 -9 -9 -9 -9 1 1 1 3 3 3 1 1 1 1

QCS7 1 0 2 2 2 2 2 2 1 1 2 2 -9 -9 1 1 1 1 2 2 1 1 1 1 2 3 1 1 1 1

QCSI 1 0 1 1 -9 -9 2 2 1 1 2 2 2 2 1 1 -9 -9 2 2 1 1 3 3 3 3 1 9 -9 -9

EM13 2 0 2 2 -9 -9 2 11 -9 -9 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 3 1 1 1 1

EM16 2 0 1 1 2 2 -9 -9 1 1 2 2 2 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 -9 -9

EM19 2 0 -9 -9 2 2 2 6 1 1 2 2 2 2 -9 -9 1 1 2 2 -9 -9 1 3 1 3 1 1 1 1

EM20 2 0 -9 -9 2 2 2 4 1 1 2 2 2 2 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 2

EM22 2 0 2 2 2 2 -9 -9 1 1 2 2 1 2 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1

EM24 2 0 -9 -9 -9 -9 2 2 1 1 2 2 1 2 -9 -9 1 1 1 2 1 1 1 1 1 1 1 1 1 1

EM4 2 0 2 2 2 2 2 2 1 1 2 2 2 2 1 1 1 1 1 2 1 1 1 1 3 3 1 1 1 9

EM8 2 0 2 2 2 2 -9 -9 1 1 2 2 -9 -9 1 1 1 1 1 2 1 1 1 3 3 3 1 1 1 1

SF10 3 0 2 2 2 2 -9 -9 1 1 2 2 2 2 1 1 -9 -9 1 1 1 2 1 1 1 1 1 1 -9 -9

SF13 3 0 2 2 2 2 2 2 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

SF16 3 0 -9 -9 2 2 2 10 1 1 2 2 2 2 1 1 -9 -9 1 1 1 1 3 6 1 1 1 8 1 1

SF19 3 0 2 2 2 2 2 2 1 1 -9 -9 -9 -9 1 1 1 1 1 1 1 1 1 1 -9 -9 1 1 1 1

SF1 3 0 -9 -9 2 2 2 2 1 1 2 2 2 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1

SF22 3 0 -9 -9 2 2 2 10 1 1 2 2 -9 -9 1 1 1 1 1 2 1 1 1 1 -9 -9 1 1 1 1

SF4 3 0 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -9 -9

SF7 3 0 -9 -9 2 2 -9 -9 1 1 2 2 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 2

TTS10 4 0 -9 -9 2 2 1 1 1 1 2 2 2 2 -9 -9 1 1 1 1 1 1 1 1 -9 -9 1 6 1 1

TTS13 4 0 2 2 2 2 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 4 -9 -9 -9 -9 1 1 1 1

TTS16 4 0 1 2 1 1 1 2 1 1 1 2 1 1 -9 -9 1 2 1 1 1 1 1 1 1 2 1 1 1 1

TTS1 4 0 -9 -9 2 2 -9 -9 1 1 2 2 1 2 1 1 -9 -9 1 1 1 1 1 1 1 3 1 1 1 1

TTS22 4 0 -9 -9 2 2 1 1 1 1 2 2 1 2 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1

TTS24 4 0 2 2 1 1 2 2 1 1 2 2 2 2 -9 -9 1 1 2 2 1 1 1 5 -9 -9 1 1 1 1

TTS5 4 0 -9 -9 2 2 2 2 1 1 2 2 2 2 1 1 1 2 1 1 1 5 1 1 -9 -9 1 3 1 1

TTS7 4 0 2 2 2 2 2 2 1 1 -9 -9 2 2 1 1 1 1 1 1 1 1 -9 -9 2 2 1 1 1 1

JYS10 5 0 2 2 2 2 -9 -9 1 1 2 2 1 2 1 1 1 3 1 2 7 7 1 1 1 1 1 1 1 2

JYS13 5 0 2 3 2 2 2 2 1 1 2 7 1 1 -9 -9 1 2 2 2 1 1 1 1 2 2 1 1 2 2

JYS16 5 0 -9 -9 2 2 2 2 1 1 2 6 1 2 1 1 3 10 1 1 1 1 1 1 1 2 1 7 -9 -9

JYS19 5 0 1 1 2 2 -9 -9 1 1 2 2 1 1 -9 -9 3 3 1 1 1 1 1 1 3 3 1 1 1 1

JYS1 5 0 1 1 2 2 1 1 1 1 2 2 1 1 -9 -9 1 1 -9 -9 1 8 1 1 1 1 1 1 1 1

JYS22 5 0 2 2 -9 -9 2 2 1 7 2 2 -9 -9 1 1 1 1 -9 -9 -9 -9 1 1 3 3 1 1 1 1

JYS4 5 0 -9 -9 2 2 -9 -9 1 1 2 2 -9 -9 1 1 2 2 2 2 1 1 1 4 2 2 1 1 -9 -9

JYS7 5 0 2 2 2 2 -9 -9 1 1 2 2 2 2 1 1 2 3 -9 -9 1 1 1 1 1 1 1 1 1 1

XC11 6 0 -9 -9 2 2 2 2 1 8 2 2 1 2 -9 -9 -9 -9 1 2 -9 -9 1 1 1 2 1 1 1 2

XC14 6 0 -9 -9 2 2 2 2 1 8 2 2 1 1 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 1

XC17 6 0 -9 -9 2 2 2 2 1 1 2 2 1 1 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 1

XC1 6 0 -9 -9 2 2 2 2 -9 -9 2 2 1 1 -9 -9 -9 -9 1 1 -9 -9 1 1 1 1 1 1 1 1

XC3 6 0 -9 -9 2 2 2 2 1 8 2 2 1 2 -9 -9 1 1 2 2 1 1 1 1 1 2 1 1 1 2

XC5 6 0 -9 -9 2 2 2 2 1 1 2 2 1 1 -9 -9 -9 -9 2 2 -9 -9 1 1 1 1 1 1 1 1

XC7 6 0 -9 -9 2 2 2 2 1 1 2 2 1 1 -9 -9 -9 -9 1 1 1 1 1 1 1 1 1 1 1 1

XC9 6 0 -9 -9 2 2 2 2 1 1 2 2 -9 -9 -9 -9 -9 -9 1 5 -9 -9 1 1 1 1 1 1 1 1

FJS10 7 0 1 1 1 2 2 2 1 1 2 2 2 2 -9 -9 3 3 1 1 1 1 -9 -9 3 3 1 1 2 2

FJS13 7 0 1 1 1 1 2 2 1 1 2 2 1 1 2 2 9 9 1 1 1 3 1 1 3 3 1 1 1 2

FJS16 7 0 1 1 1 2 2 2 1 1 2 2 1 2 1 1 1 1 1 1 1 3 1 1 3 3 1 1 2 2

FJS19 7 0 -9 -9 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 1 1 1 3 3 1 1 2 2

FJS1 7 0 1 1 1 1 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 3 3 1 1 1 2

FJS22 7 0 1 1 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 1 -9 -9 -9 -9 1 1 -9 -9

FJS4 7 0 1 1 1 2 -9 -9 1 1 2 2 2 2 1 1 1 3 1 1 1 1 1 1 -9 -9 1 1 1 1

FJS7 7 0 1 1 1 1 2 2 1 1 2 2 1 1 1 2 1 9 1 1 1 1 1 1 -9 -9 1 1 2 2

DYS11 8 0 1 1 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2

DYS15 8 0 1 1 1 1 2 2 1 1 2 2 1 2 1 1 1 1 1 1 1 1 1 1 3 3 1 1 2 2

DYS1 8 0 1 1 1 2 2 3 1 1 2 2 2 2 1 1 1 1 1 1 1 1 1 2 3 3 1 2 2 2

DYS21 8 0 1 1 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 3 1 2 3 3 1 1 -9 -9

DYS3 8 0 1 1 1 1 2 2 1 1 2 2 1 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2

DYS5 8 0 1 1 1 1 2 6 1 1 -9 -9 1 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2

DYS7 8 0 1 1 1 1 2 2 1 4 2 2 2 2 1 1 1 7 1 1 1 1 1 2 3 3 1 1 2 2

DYS9 8 0 1 1 1 1 -9 -9 1 1 2 8 2 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2

JGS11 9 0 -9 -9 2 2 5 5 1 1 -9 -9 1 1 2 2 1 1 1 1 -9 -9 1 2 -9 -9 1 3 1 1

JGS13 9 0 1 1 2 2 2 2 1 1 2 3 1 1 2 2 1 4 1 1 3 3 1 2 -9 -9 1 3 1 1

JGS16 9 0 1 1 2 2 2 2 1 1 3 3 1 1 2 2 1 1 1 1 3 3 1 2 3 3 1 3 1 1

JGS1 9 0 1 1 2 11 5 5 1 1 3 3 1 1 2 2 4 4 1 1 1 1 1 2 3 3 1 3 1 1

JGS3 9 0 1 1 2 2 -9 -9 1 1 2 3 1 1 2 2 4 4 1 1 -9 -9 1 2 -9 -9 1 3 1 1

JGS5 9 0 1 1 2 2 5 5 1 1 2 3 1 1 2 2 1 1 1 1 -9 -9 1 2 3 3 1 3 1 1

JGS7 9 0 1 1 2 2 -9 -9 1 1 3 3 1 1 2 2 -9 -9 1 1 3 3 1 2 3 3 3 3 1 1

JGS9 9 0 -9 -9 -9 -9 2 5 1 1 3 3 1 1 2 2 -9 -9 1 1 -9 -9 1 1 -9 -9 3 3 1 1

GT11 10 0 1 1 2 9 2 8 1 1 2 3 1 4 2 2 1 4 1 1 1 3 -9 -9 -9 -9 1 1 1 2

GT13 10 0 1 1 2 6 7 8 3 3 -9 -9 1 1 1 2 4 4 1 6 3 3 2 2 3 3 4 4 1 6

GT17 10 0 1 1 2 2 7 7 3 3 2 2 1 9 1 1 1 4 1 1 1 3 -9 -9 3 3 1 1 -9 -9

GT19 10 0 1 1 2 4 -9 -9 3 3 2 2 1 1 1 1 1 4 1 4 3 3 2 2 3 3 4 4 1 1

GT1 10 0 1 1 2 2 7 7 3 3 2 2 1 1 1 1 1 8 1 1 1 3 2 2 3 3 1 1 1 5

GT3 10 0 1 2 2 2 5 8 -9 -9 2 3 1 4 2 2 1 4 1 1 1 3 -9 -9 3 3 4 4 1 8

GT5 10 0 1 1 2 7 2 9 1 3 2 3 1 1 2 2 4 4 1 7 3 3 2 2 3 3 1 1 1 7

GT9 10 0 1 1 2 6 8 8 3 3 2 3 1 4 1 2 1 4 1 8 1 3 2 2 3 3 4 4 1 1

MX13 11 0 1 1 2 2 2 2 1 1 2 3 1 7 1 2 1 1 1 1 3 3 2 2 -9 -9 1 4 1 1

MX1 11 0 1 1 2 2 -9 -9 1 1 3 3 1 4 2 2 1 1 1 1 3 3 2 2 -9 -9 1 1 1 1

MX25 11 0 1 1 2 2 2 2 1 1 2 3 1 1 2 2 -9 -9 1 1 3 3 1 2 3 3 1 1 1 1

MX29 11 0 1 1 2 5 5 5 1 1 3 3 1 3 2 2 -9 -9 1 1 3 3 1 2 1 3 1 1 -9 -9

MX2 11 0 1 1 -9 -9 2 2 1 1 3 3 1 1 2 2 1 5 1 1 3 5 2 2 3 3 1 4 1 1

MX33 11 0 1 1 2 2 5 5 1 11 -9 -9 1 4 2 2 1 1 1 1 3 3 2 2 3 3 4 4 1 1

MX5 11 0 1 1 2 2 2 2 1 1 2 2 1 4 2 2 1 1 1 1 -9 -9 1 1 -9 -9 1 1 1 1

MX9 11 0 1 1 2 2 2 5 -9 -9 2 2 1 1 2 2 1 1 1 1 3 3 2 2 3 3 1 1 1 1

FT11 12 0 1 1 2 2 5 7 1 9 2 3 1 8 2 2 1 4 1 1 3 3 2 2 3 3 1 3 1 2

FT13 12 0 1 1 2 3 -9 -9 1 3 2 3 1 1 2 2 4 6 1 1 3 3 2 2 3 3 1 1 1 1

FT16 12 0 1 1 2 8 -9 -9 1 1 2 4 1 5 1 2 1 8 1 1 3 6 2 2 3 3 3 3 1 1

FT20 12 0 1 1 2 2 -9 -9 1 1 2 2 1 1 2 2 1 4 1 1 3 3 2 2 3 3 1 5 1 1

FT21 12 0 1 1 2 2 2 8 1 6 2 5 -9 -9 2 2 1 1 1 1 3 3 2 2 3 3 -9 -9 1 2

FT3 12 0 1 1 2 2 5 5 1 1 2 5 1 2 1 2 -9 -9 1 1 3 6 2 2 3 3 1 3 -9 -9

FT5 12 0 1 1 2 2 5 5 1 2 2 3 1 1 2 2 1 4 1 1 3 3 2 2 1 3 1 4 1 1

FT9 12 0 1 1 2 2 2 7 1 1 -9 -9 1 3 2 2 1 4 1 1 3 3 2 2 3 3 4 5 1 1

GS13 13 0 1 1 2 2 2 2 1 1 2 3 1 1 2 2 1 6 1 1 3 3 2 2 3 3 1 3 1 1

GS1 13 0 1 1 2 2 -9 -9 1 5 3 3 1 1 2 2 6 6 1 3 3 3 1 1 3 3 1 3 1 3

GS25 13 0 1 1 2 2 2 2 -9 -9 2 2 1 1 2 2 1 6 1 1 1 3 2 2 3 3 1 3 1 1

GS27 13 0 1 1 2 10 2 2 1 3 2 3 1 6 2 2 1 1 1 1 3 3 2 2 3 3 1 3 1 10

GS28 13 0 1 1 2 2 2 2 1 10 3 3 1 1 2 2 1 1 1 1 3 3 2 2 3 3 1 2 1 1

GS2 13 0 1 1 -9 -9 -9 -9 1 1 2 3 1 1 2 2 1 4 1 1 3 3 2 2 3 3 3 3 -9 -9

GS3 13 0 1 1 -9 -9 -9 -9 1 1 2 3 1 1 1 2 -9 -9 1 1 3 3 -9 -9 3 3 -9 -9 1 4

GS9 13 0 1 1 2 2 2 2 1 1 2 2 1 1 2 2 4 4 1 1 3 3 2 2 1 3 1 2 1 1

      Thank you,

      Ye

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