Question: Strange Files With EIGENSOFT smartpca
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gravatar for dxm275
24 months ago by
dxm2750
dxm2750 wrote:

Hello, I am having some strange problems with the smartpca.perl. I have the following files:

MyLungGwas.bim MyLungGwas.bed MyLungGwas.fam

and wanted to perform a pca on them. So I used the following command:

smartpca.perl -i MyLungGwas.bed -a MyLungGwas.bim -b MyLungGwas.fam \
  -p MyLungGwas.plot -e MyLungGwas.eval -o MyLungGwas.pca -q NO \
  -l MyLungGwas-smartpca.log smartpca -p MyLungGwas.pca.par > MyLungGwas-smartpca.log

I got several of the output files that I expected and quite a few that I don't understand. These new files look like:

MyLungGwas.pca.evec.1:2:\213U\374Hc\322H\301\342\002H\003U؋\022\215\024\021\211\020\203E\374\001\213E\374;E\324|\302\311\303UH\211\345SH\211}\340H\211u\330H\211UЉM\314\307E\364

MyLungGwas.pca.evec.1:2:\213U\374Hc\322H\301\342\003H\003U\330\362\017\020\002\362\017X\301\362\017\021

I've also using

MyLungGwas.bed MyLungGwas.pedsnp MyLungGwas.pedind

with similar results.

I'm also seeing a file that looks like this afterward: core.16353

Can anyone tell me exactly what is going on here? Thanks, Diego

pca gwas eigensoft • 575 views
ADD COMMENTlink modified 24 months ago by h.mon29k • written 24 months ago by dxm2750
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