PLINK does not uncompress GZ file automatically, why?
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6.2 years ago
odeta.xjd • 0

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

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 • 4.0k views
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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?

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

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

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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

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

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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

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

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I presume you use mac?

brew install gzip

Or just http://www.gzip.org/

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I installed gzip:

brew install gzip

==> Installing gzip from homebrew/homebrew-dupes

######################################################################## 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?