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Running Eigenstrat?

Hi,

I am trying to run Eigenstrat on a set of ~400,000 SNPs.

The software suite provides a wrapper perl script (smartpca.perl) which takes command line arguments, formats a parameter file and calls smartpca.

When the program reaches the point of calling smartpca, I get an error saying 'Cannot execute binary'. I am running Fedora 13. Are there extra packages, compilers, etc. that I may require in order to execute smartpca?

Thanks, D.

error
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written by Darren J. Fitzpatrick Darren J. Fitzpatrick

2 answers

I posted the solution to my qualm in my blog.

Hopefully it may be helpful to others.

D.

• 3 views • link
updated by Ram Ram • written by Darren J. Fitzpatrick Darren J. Fitzpatrick

@Darren, the link seems to not be working. Care to share the results?

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written by biohack92 biohack92

from the source code: http://genetsim.org/class/EIG3.0/bin/smartpca.perl I can see that this script call several external programs (ploteig, evec2pca.perl, smartpca) using a command system(...) .

Please check that those binaries are located in the $PATH variable.

• 2 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Yep - the path is correct. I believe I have solved it and will post the details of my installation when I am absolutely certain. D.

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written by Darren J. Fitzpatrick Darren J. Fitzpatrick

@Darren Care to share the results of your troubleshooting?

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written by biohack92 biohack92

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