Question: Run smartpca from eigensoft
0
gravatar for elena.bacchelli
3.3 years ago by
elena.bacchelli0 wrote:

Hi, I have encountered an error trying to run smartpca from eigensoft. I have converted my PLINK ped and map files to eigensoft file format using convertf and then I used the following command line to run smartpca:

perl smartpca.pl -i mc_aims.eigenstratgeno -a mc_aims.snp -b mc_aims.ind -o mc_aims.pca -p mc_aims.plot -m 0 -e mc_aims.eval -l mc_aims.log -k 2 -t 2

but I got this error:

smartpca -p mc_aims.pca.par >mc_aims.log smartpca: symbol lookup error: smartpca: undefined symbol: dspev_ ploteig -i mc_aims.pca.evec -c 1:2 -p -x -y -o mc_aims.plot.xtxt evec2pca.perl 2 mc_aims.pca.evec mc_aims.ind mc_aims.pca

It is the same if I use the example files:

perl smartpca.pl -i example.eigenstratgeno -a example.snp -b example.ind -o example.pca -p example.plot -m 0 -e example.eval -l pca_example.log -k 2 -t 2 -s 6

smartpca -p example.pca.par >pca_example.log smartpca: symbol lookup error: smartpca: undefined symbol: dspev_ ploteig -i example.pca.evec -c 1:2 -p -x -y -o example.plot.xtxt evec2pca.perl 10 example.pca.evec example.ind example.pca

So now I'm stuck....Could someone help me please?

Thank you!! Cheers, Elena

ADD COMMENTlink written 3.3 years ago by elena.bacchelli0

The error indicates a missing dependency. Did you install binaries or compiled the software from source ? In the former case, make sure the binaries are for your system otherwise compile from source. In the latter case, check that all dependencies are satisfied. dspev is a LAPACK function so the message suggests a possible problem linking to LAPACK.

ADD REPLYlink written 3.3 years ago by Jean-Karim Heriche20k
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