Plink starts up then ends terminal session

[bob lalonde]

Hi Guys: 

Plink worked 2 days ago just fine. When I tried to run it yesterday I got the following:

Last login: Wed Jul 20 09:46:09 on console

[MacBook-Air:~] todd% /Bob\'s\ Stuff/Eurytoma/plink_mac_20220402/plink ; exit;

PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/

(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3

  plink <input flag(s)...> [command flag(s)...] [other flag(s)...]

  plink --help [flag name(s)...]

Commands include --make-bed, --recode, --flip-scan, --merge-list,

--write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,

--hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,

--blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,

--rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,

--model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,

--make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,

--meta-analysis, --epistasis, --fast-epistasis, and --score.

"plink --help | more" describes all functions (warning: long).

logout

[Process completed]

In a nutshell, it just started up then shut itself down. I moved my data to a new computer, downloaded Plink to it and tried again. Same result. 

Thoughts?

[Christopher Chang]

Are you referring to the PuTTY Link program (https://the.earth.li/~sgtatham/putty/0.58/htmldoc/Chapter7.html )?  If so, you installed the wrong program named "plink".

[Chris Chang]

Then you should know that plink ISN'T SUPPOSED TO DO ANYTHING if you don't provide any command-line flags.

On Wed, Jul 20, 2022 at 11:37 AM bob lalonde <robert....@ubc.ca> wrote:

nope

[Chris Chang]

The "; exit" at the end of your command line explicitly ensures that you don't get the command prompt that you'd normally have.

On Wed, Jul 20, 2022 at 12:15 PM Lalonde, Robert <robert....@ubc.ca> wrote:

Yes, I know that. As I said, it worked fine two days ago. What I forgot to mention here is that I don’t get a terminal prompt after the [Process completed] line, so I can’t put in a command line. 

Bob

On Jul 20, 2022, at 11:39 AM, Chris Chang <chrch...@gmail.com> wrote:

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Let's not burn the universities yet. After all, the damage they do might be worse. 

Mencken, H. L. 

Dr. R.G. Lalonde

Department of Biology

University of British Columbia - Okanagan

1177 Research Road, Kelowna, BC

V1V 1V7

(250) 807-8764

[Chris Chang]

The standard workflow on Windows is to open a command prompt, and then type "plink" inside the command prompt.  You are never supposed to "just click on plink.exe".

On Wed, Jul 20, 2022 at 12:34 PM Lalonde, Robert <robert....@ubc.ca> wrote:

I see that, but I didn’t do that. All I did was right click on the Plink EXE file, and opened it in terminal. No typing!

Bob

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