search

DReichLab / EIG

Eigen tools by Nick Patterson and Alkes Price lab
Other
180 stars 60 forks source link

XTX has zero trace (perhaps no data) #68

Closed sahwa closed 3 years ago

sahwa commented 3 years ago

I have recieved this cryptic error message:

XTX has zero trace (perhaps no data)

The files were produced by running convertf on .ped/.map files. I have tried removing the 'chr' prefix from the snpfile, but it makes no difference. What is the cause of this?

Log:

### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
genotypename: example.eigenstratgeno
snpname: example.snp
indivname: example.ind
evecoutname: pca.evec.txt
evaloutname: pca.eval.txt
poplistname: pops.txt
lsqproject: YES
## smartpca version: 18140
norm used

lsqproject used
snps deleted (nodata): 455918.  deletesnpoutname: for detailsnumber of samples used: 0 number of snps used: 0
number of pops for axes: 22
Using 1 thread, and partial sum lookup algorithm.
total number of snps killed in pass: 0  used: 0
fatalx:
XTX has zero trace (perhaps no data)
Aborted (core dumped)

example.snp

1:752566[b37]   chr1    0.007526    752566  A   G
1:1005806[b37]  chr1    0.010058    1005806 C   T
1:1018704[b37]  chr1    0.010187    1018704 G   A
1:1021415[b37]  chr1    0.010214    1021415 G   A
1:1030565[b37]  chr1    0.010306    1030565 C   T

example.ind

10:LBK U 10:LBK
HB:croatian1 U HB:croatian1
HB:croatian2 U HB:croatian2
HB:croatian3 U HB:croatian3

example.eigenstratgeno

299999999999999999992212201211122222211111222212122221122221202122222221222222222222222222222221222222222222222222222121221111211112222222222211120222222222222222222222222122202221112222021222122999999999999999992222222211112222212122222222222222222212122221122212222221122102222121211112121222212222222222122222222222222222222222222222222222222222222222222222222222222222222222222222222222222212222221211222222212222992922221990922111299922222219291111112999922222
199999999999999999990012111212222222221120212112221221212222222022222222111212122212222122222221221212212222121122222112222122122211222222122122122112222222222222221121222201122222222222122222210999999999999999992222110222010222122222222212122222211222222222221221221122222121111221222222122222222222121100222222121111212122222212122112202212221220222222222221212222212121221222212222021221212120222222222212212121221990992212929222222292292222229999222221999992111
199999999999999999990011001110020212111010202111221221211012212011121220011211121212220111211211221200001022120121211010111100112101222122122011012012101111112120110100222101122102222211121121110999999999999999992210000001000011022112002212022121211221212122121211220122220021111221221212022122211221121000202112000001001112122011111012101211121220212221022121200102111121111012100021021121202020202212221211211011221992299110900900000292992222229992222221902991111
1993zsj123 commented 1 year ago

I have encountered the same problem. Have you resolved it?

bumblenick commented 12 months ago

You have no valid data.

Nick

On Thu, Nov 30, 2023 at 3:49 AM 1993zsj123 @.***> wrote:

I have encountered the same problem. Have you resolved it?

— Reply to this email directly, view it on GitHub https://github.com/DReichLab/EIG/issues/68#issuecomment-1833337572, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEE77BZU4XVUI4LC4EI7LJDYHBCDDAVCNFSM5AI6TSZKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBTGMZTGNZVG4ZA . You are receiving this because you are subscribed to this thread.Message ID: @.***>