I have encountered an error trying to run smartpca from eigensoft.
I have converted ped file of my SNPs to eigensoft file format using fcgene and entered the following command line
to run smartpca:
perl ./bin/smartpca.perl -i out_eigensoft.ped -a out_eigensoft.pedsnp -b out_eigensoft.pedind -m 0 -o out.pca -p out.plot -l out.log -e out.eval
When I ran it, it gives an error claiming that:
OOPS couldn't open file out.pca.evec for reading at ./bin/smartpca.perl line 65.
All the files are in the bin folder, so I believe this is not the path problem...
I have been stuck for days now. Could someone help me please?