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DReichLab / EIG

Eigen tools by Nick Patterson and Alkes Price lab
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OOPS -i flag not specified at /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21. #35

Open bk11-lab opened 5 years ago

bk11-lab commented 5 years ago

I tried to run smartpca.pl for this par file and every input files are in the same directory from where I tried to run smartpca.pl. However, I get error every time saying OOPS -i flag not specified at /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21. My Par file looks like genotypename: p1_nor_non_nor_sicca_merged.bed snpname: p1_nor_non_nor_sicca_merged.bim indivname: p1_nor_non_nor_sicca_merged.fam evecoutname: p1_nor_non_nor_sicca_merged.pca.evec evaloutname: p1_nor_non_nor_sicca_merged.eval altnormstyle: NO numoutevec: 10 numoutlieriter: 5 numoutlierevec: 10 outliersigmathresh: 6 qtmode: NO familynames: NO

Please some one could help me. I will appreciate any help

bumblenick commented 5 years ago

Probably you should be running smartpca not smartpca.pl

On Thu, Apr 25, 2019 at 5:37 PM Bhuwan Khatri notifications@github.com wrote:

I tried to run smartpca.pl for this par file and every input files are in the same directory from where I tried to run smartpca.pl. However, I get error every time saying OOPS -i flag not specified at /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21. My Par file looks like genotypename: p1_nor_non_nor_sicca_merged.bed snpname: p1_nor_non_nor_sicca_merged.bim indivname: p1_nor_non_nor_sicca_merged.fam evecoutname: p1_nor_non_nor_sicca_merged.pca.evec evaloutname: p1_nor_non_nor_sicca_merged.eval altnormstyle: NO numoutevec: 10 numoutlieriter: 5 numoutlierevec: 10 outliersigmathresh: 6 qtmode: NO familynames: NO

Please some one could help me. I will appreciate any help

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bk11-lab commented 5 years ago

smartpca.perl is the executable in my system and not smartpca or smartpca.pl.

petrelharp commented 4 years ago

The smartpca executable is found in the src/eigensrc/ directory after you run make; and would be put somewhere in your PATH if make install works.