Question

Unused command line option: --make-just-fam

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3.1 years ago

suraj.adewale1 • 0

We are trying to run the plink command for QC

plink \
--bfile EUR \
--maf 0.01 \
--hwe 1e-6 \
--geno 0.01 \
--mind 0.01 \
--write-snplist \
--make-just-fam \
--out EUR.QC

however, it gives us an error: ERROR: Problem parsing the command line arguments. Please what may be the possible cause of the error. I am using the Cygwin platform on windows.

plink GWAS linux • 1.5k views

ADD COMMENT • link updated 3.1 years ago by davidenoma ▴ 50 • written 3.1 years ago by suraj.adewale1 • 0

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Can you at least show the full error log?

ADD REPLY • link 3.1 years ago by Sam ★ 4.7k

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This is the full error output from plink. only that ** Unused command line option: --make-just-fam

ADD REPLY • link 3.1 years ago by suraj.adewale1 • 0

score 2 · Answer 1 · 2021-03-10

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3.1 years ago

chrchang523 10k

That error message is from plink 1.07. This flag requires plink 1.9.

ADD COMMENT • link 3.1 years ago by chrchang523 10k

score 1 · Answer 2 · 2021-03-11

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3.1 years ago

davidenoma ▴ 50

I tried the issue on my virtual machine and it turns out that you have to install the plink 1.90 beta version from https://www.cog-genomics.org/plink/

ADD COMMENT • link 3.1 years ago by davidenoma ▴ 50