Question

Running Eigenstrat?

1

Entering edit mode

13.7 years ago

Darren J. Fitzpatrick ★ 1.1k

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 • 9.3k views

ADD COMMENT • link 13.7 years ago by Darren J. Fitzpatrick ★ 1.1k

Ram · Answer 1 · 2011-03-28

3

Entering edit mode

13.7 years ago

Darren J. Fitzpatrick ★ 1.1k

I posted the solution to my qualm in my blog.

Hopefully it may be helpful to others.

D.

ADD COMMENT • link updated 5.2 years ago by Ram 44k • written 13.7 years ago by Darren J. Fitzpatrick ★ 1.1k

0

Entering edit mode

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

ADD REPLY • link 9.1 years ago by biohack92 ▴ 170

score 0 · Answer 2 · 2011-03-28

0

Entering edit mode

13.7 years ago

Pierre Lindenbaum 164k

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.

ADD COMMENT • link 13.7 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

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.