Question: errors in running smartpca
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Entering edit mode
18 months ago
sam980406 • 0

Hello! I have encountered an error trying to run smartpca from eigensoft. I made a file for smartpca named 'eigenstrat_run'

genotypename :938HGDP_forPCA.eigenstratgeno

snpname :938HGDP_forPCA.snp

indivname :938HGDP_forPCA.ind

evecoutname :result.evec

evaloutname : result.eval

altnormstyle : NO

numoutevec : 20

numoutlieriter : 0

poplistname : pop.txt

and I tried to run smartpca with this file, but I got this error message like this. What's the matter with my program? Help me!

parameter file: eigenstrat_run **warning: dubious parameter, please check the parameter name genotypename

**warning: dubious parameter, please check the parameter name snpname

**warning: dubious parameter, please check the parameter name indivname

**warning: dubious parameter, please check the parameter name evecoutname

**warning: dubious parameter, please check the parameter name evaloutname

**warning: dubious parameter, please check the parameter name altnormstyle

**warning: dubious parameter, please check the parameter name numoutevec

**warning: dubious parameter, please check the parameter name numoutlieriter

**warning: dubious parameter, please check the parameter name poplistname

THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename :938HGDP_forPCA.eigenstratgeno

snpname :938HGDP_forPCA.snp

indivname :938HGDP_forPCA.ind

evecoutname :result.evec

evaloutname : result.eval

altnormstyle : NO

numoutevec : 20

numoutlieriter : 0

poplistname : pop.txt

smartpca version: 16000 norm used

fatalx: (getsnps) null snpnameAborted (core dumped)

smartpca eigenstrat • 549 views
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Entering edit mode

that software seems to be too old and unmaintained (last push was 7 years ago), I would suggest you to use R (check FactoMineR and princomp)

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