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)
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)