Question: PLINK does not uncompress GZ file automatically, why?
0
gravatar for odeta.xjd
2.9 years ago by
odeta.xjd0
United Kingdom
odeta.xjd0 wrote:

I'm new to plink, I read the plink online instruction that plink will uncompress gz file automatically, but when I use plink:

./plink --bfile mydata

it gives me the following error:

ERROR: No file [ mydata.fam ] exists.

Only when I uncompress my .fam .bim .bed files, the command works.

I am very confused because the dataset is large and uncompress them takes up many space on my mac. Can anyone tell my why my plink does not uncompress gz files?

 

snp plink gz • 1.7k views
ADD COMMENTlink written 2.9 years ago by odeta.xjd0

The .bed is already a binary format, and is already meant to be a sort of compression of the data. Why do you want to compress it? How much do you save after the compression?
 

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Giovanni M Dall'Olio26k

I just feel weird since plink is supposed to work with .gz file but it does not work on my laptop

ADD REPLYlink written 2.9 years ago by odeta.xjd0

Are you using the same version in both computers? Maybe you have a missing or misconfigured gzip library.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Giovanni M Dall'Olio26k

I am sorry I totally don't understand what "a missing or misconfigured gzip library" mean, and if yes how can I solve this problem? Thank you very much for answering

ADD REPLYlink written 2.9 years ago by odeta.xjd0

dont compress the bed bim or fam files. leave them as is. they are in binary format. they are already HIGHLY condensed.

ADD REPLYlink written 2.9 years ago by Vincent Laufer890

Basically what Giovanni mean is that the gzip library installed on the two different computer may be different. Most likely that you didn't even have the gzip library installed in on your laptop. That's why plink cannot work with the gzip data 

ADD REPLYlink written 2.9 years ago by Sam2.1k

Thank you for the reply, and how can I install a gzip library?

ADD REPLYlink written 2.9 years ago by odeta.xjd0

I presume you use mac? 

brew install gzip

Or just http://www.gzip.org/

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Sam2.1k

I installed gzip:

brew install gzip

==> Installing gzip from homebrew/homebrew-dupes

==> Downloading https://homebrew.bintray.com/bottles-dupes/gzip-1.6.yosemite.bot

######################################################################## 100.0%

==> Pouring gzip-1.6.yosemite.bottle.1.tar.gz

🍺  /usr/local/Cellar/gzip/1.6: 33 files, 404K

But plink still can't work with .gz files. Shall I restart my mac maybe?

ADD REPLYlink written 2.9 years ago by odeta.xjd0
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