Error with smarteigenstrat.perl accepting pca output from smartpca.perl

[harrsha4]

kuretlab@Synuclein:~/Bayesian/EIG/bin$ $ ./smarteigenstrat.perl -output.geno -a output.snp -b output.ind -p output.evec -o output.chiseq -l output.log -k 10
smarteigenstrat -p output.chiseq.par >output.log
OOPS: output.evec contains too many entries

Hello,
I ran smartpca as instructed on my WGS dataset (349 individuals, 20 million SNPs). The smartpca.perl wrapper ran fine producing 10 principal components in an .evec file. However, when loading the pca file into smarteigenstrat.perl, the aforementioned error was returned. What I find interesting is that after outlier removal by smartpca, the .ind file had 349 individuals even when sigma was at default value and the log file noted the removal of outliers (around 30 individuals). Is there something I can do to fix this. Thanks in advance

[kristjanmoore]

Try -i output.geno instead of -output.geno.

[Ajeet1699]

Hi,

I am trying to run the eigenstrat, and it is giving me error.

~/software/EIG-7.2.1/bin/smarteigenstrat.perl -i convertf_out.eigenstratgeno -a convertf_out.snp -b convertf_out.ind -p smartpca.pca.evec -o smarteigenstrat.chisq -l smarteigenstrat.log -k 10
~/software/EIG-7.2.1/bin/smarteigenstrat -p smarteigenstrat.chisq.par >smarteigenstrat.log
OOPS: smartpca.pca.evec contains too many entries
head -2 smartpca.pca.evec

#eigvals: 1.571 1.178 1.128 1.111 1.092 1.085 1.076 1.072 1.069 1.066
SA_111__snpArray 0.0013 0.0306 -0.1754 -0.0894 0.1311 0.0199 0.0054 0.1591 0.1337 0.1837 ???
`
Any help with that? Thanks.

[bumblenick]

With regrets this perl script is onsolescent and no longer being maintained. Nick Patterson

…

On Fri, Feb 7, 2025 at 9:31 AM Ajeet1699 ***@***.***> wrote: Hi, I am trying to run the eigenstrat, and it is giving me error. ~/software/EIG-7.2.1/bin/smarteigenstrat.perl -i convertf_out.eigenstratgeno -a convertf_out.snp -b convertf_out.ind -p smartpca.pca.evec -o smarteigenstrat.chisq -l smarteigenstrat.log -k 10 ~/software/EIG-7.2.1/bin/smarteigenstrat -p smarteigenstrat.chisq.par >smarteigenstrat.log OOPS: smartpca.pca.evec contains too many entries `head -2 smartpca.pca.evec #eigvals: 1.571 1.178 1.128 1.111 1.092 1.085 1.076 1.072 1.069 1.066 SA_111__snpArray 0.0013 0.0306 -0.1754 -0.0894 0.1311 0.0199 0.0054 0.1591 0.1337 0.1837 ??? ` Any help with that? Thanks. — Reply to this email directly, view it on GitHub <#75 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77BZZTO55W2QP5ZRILWT2OS7THAVCNFSM6AAAAABWWC73U2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNBTGEYDEOJTGM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Ajeet1699]

I have also tried without perl.

~/software/EIG-7.2.1/bin/smarteigenstrat -p smarteigenstrat.chisq.par
parameter file: smarteigenstrat.chisq.par
genotypename: convertf_out.eigenstratgeno
snpname: convertf_out.snp
indivname: convertf_out.ind
pcaname: smartpca.pca.evec
outputname: smarteigenstrat.chisq
numeigs: 10
qtmode: NO
OOPS: smartpca.pca.evec contains too many entries