Entering edit mode
19 months ago
rosy
•
0
I am using eigensoft (smartPCA) to do PCA by
./smartpca.perl -i my.bed -a my.pedsnp -b my.pedind -o output.pca -p output.plot -e output.eval -m 10 -s 5 -l output.log
I also tried using example files in CONVERTF folder
./smartpca.perl -i example.bed -a example.pedsnp -b example.pedind -o output.pca -p output.plot -e output.eval -m 10 -s 5 -l output.log
but I got this error in both the cases
sh: smartpca: command not found
OOPS couldn't open file output.pca.evec for reading at ./smartpca.perl line 65. The eigensoft version I am using is latest(7.2.1) please help me to resolve this issue
check your PATH https://linuxhint.com/path_in_bash/