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

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

Start by reproducing the shown smarteigenstrat.perl command with output.evec, output.ind, and output.chiseq.par, then inspect how smartpca.perl produces output.evec and how smarteigenstrat.perl reads it. Compare the .evec entry count with the outlier-removal information in the log; done means the PCA output is accepted or the incompatibility and required input format are clearly documented.