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eigensoft smartpca error "OOPS -i flag not specified at smartpca.perl line 21

Hi,

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!

Lauren

smartpca error -i flag eigensoft
• 5,279 views • link
updated by Ram Ram • written by laurenvw • laurenvw

-i is the genotypes file. What is your full command for smartpca.perl?

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updated by Ram Ram • written by rbagnall rbagnall

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.
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updated by Ram Ram • written by laurenvw • laurenvw

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