Question: bim and fam downloaded as .txt files, won't work with PLINK?
0
gravatar for maya123z
2.1 years ago by
maya123z30
maya123z30 wrote:

Fair warning, I am very new to PLINK and to the command line in general. I downloaded my bed, bim, and fam files from this website. However, the bim and fam files are formatted as .txt files. As a result, when I type

plink --bfile dgrp2

it returns 'ERROR: No such file [ dgrp2.fam ] exists' because the file is named dgrp2.fam.txt. I tried renaming the files without the "txt" but it wouldn't let me. Advice would be greatly appreciated.

snp plink gwas • 958 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by maya123z30
2
gravatar for genomax
2.1 years ago by
genomax80k
United States
genomax80k wrote:

I recently discovered that macOS High Sierra did this on some downloaded files (and would also not allow me to rename affected files via finder). I think the best option is to open a terminal window, cd to the directory where these files are and then do mv dgrp2.fam.txt dgrp2.fam to rename the file. If that does not work then you may have to do sudo mv dgrp2.fam.txt dgrp2.fam

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by genomax80k

That fixed it! Thanks!

ADD REPLYlink written 2.1 years ago by maya123z30

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 2.1 years ago by WouterDeCoster43k
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