OOPS -i flag not specified at /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21.

[bk11-lab]

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]

Probably you should be running smartpca not smartpca.pl

…

On Thu, Apr 25, 2019 at 5:37 PM Bhuwan Khatri ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#35>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEE77B2UIR4GMDWTJVNCY4TPSIQB7ANCNFSM4HIQ3SAA> .

[bk11-lab]

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

[petrelharp]

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.