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DReichLab / EIG

Eigen tools by Nick Patterson and Alkes Price lab
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elliptical confidence not calculated #106

Open Kelzor opened 3 months ago

Kelzor commented 3 months ago

Hello!

I am running smartpca with the following par file. The run goes to completion, and I get .evec and .eval files. But the confidence ellipses are not being calculated and no ellout file is generated. No errors are thrown. Am I doing something wrong with the parameter setup?

genotypename: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.geno
snpname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.snp
indivname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.ind
evecoutname: ellconfnoshrinkWiaHCayonuWEurasiaHO.evec
evaloutname: ellconfnoshrinkWiaHCayonuWEurasiaHO.eval
lsqproject: YES
poplistname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WestEurasiapoplistmodern.txt
outliermode: 0
numoutevec: 2
elllistname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHList.txt
elloutname: WiaHell95.out
ellconf: 0.95

Thanks, Kelly

bumblenick commented 3 months ago

I intend to put out a new release of smartpca in a couple of weeks. Look out for it. In my in house test version the ellipse confidence is working. In your parameter file, please delete outliermode: This is an obscure parameter I haven't used for years.

and try numoutlier: 0

Nick

On Mon, Jul 29, 2024 at 10:44 AM Kelly Blevins @.***> wrote:

Hello!

I am running smartpca with the following par file, but the confidence ellipses are not being calculated and no ellout file is generated. Am I doing something wrong?

genotypename: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.geno snpname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.snp indivname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.ind evecoutname: ellconfnoshrinkWiaHCayonuWEurasiaHO.evec evaloutname: ellconfnoshrinkWiaHCayonuWEurasiaHO.eval poplistname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WestEurasiapoplistmodern.txt outliermode: 0 numoutevec: 2 elllistname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHList.txt elloutname: WiaHell95.out ellconf: 0.95

Thanks, Kelly

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Kelzor commented 3 months ago

Hi, Nick. I updated from 7.2 to 8.0 and removed outliermode: It works now. Probably the version was the issue?

Big thanks for the quick response!

bumblenick commented 3 months ago

Very likely; by the way a new release of ADMIXTOOLS will come out in the next few days followed shorty after by smartpca

Nick

On Tue, Jul 30, 2024 at 1:00 PM Kelly Blevins @.***> wrote:

Hi, Nick. I updated from 7.2 to 8.0 and removed outliermode: It works now. Probably the version was the issue?

Big thanks for the quick response!

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