Question: eigensoft smartpca error "OOPS -i flag not specified at smartpca.perl line 21
gravatar for laurenvw
4.8 years ago by
laurenvw20 wrote:


I'm trying to run Eigensoft's smartPCA on some data I just converted from vcf files to eigensoft format using PGDSpider. When I try to run it I immediately get back the error "OOPS -i flag not specified at EIG6.0.1/bin/smartpca.perl line 21." I have tried searching online for answers, but I can't seem to find anyone who has had the same error as me. Any guidance would be appreciated!


smartpca error -i flag eigensoft • 2.9k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by laurenvw20

-i is the genotypes file 

What is your full command for smartpca.perl?

ADD REPLYlink written 4.8 years ago by rbagnall1.7k

So I tried a few more things, right now my full command is "~/EIG6.0.1/bin/smartpca.perl -i mincov7_NS234_bisnps.eigen.geno -a mincov7_NS234_bisnps.eigen.snp -b minvov7_NS234_bisnps.eigen.ind -k -e mincov7_NS234_bisnps.eval -l mincov7_NS234_bisnps.log -m -s -o mincov7_NS234_bisnps.pca -p mincov7_NS234_bisnps.plot"  

I'm no longer getting the "-i flag not specified error", I'm getting the errors: 

smartpca -p .par >

sh: -c: line 0: syntax error near unexpected token `newline'

sh: -c: line 0: `smartpca -p .par >'

OOPS couldn't open file .evec for reading at /Users/ericagoetze/EIG6.0.1/bin/smartpca.perl line 65.

ADD REPLYlink written 4.8 years ago by laurenvw20
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