Plink: Problem connecting to web

[WonderingAtWork]

Dear all,
I am using plink but it cannot connect to the web (error message: "Problem connecting to web"). Usually that doesn't matter but now I'd like to use plink's annotation function ("Connecting to web... failed connection"). Do you know how to fix that?
Thanks a lot!

[vivek_]

You could just use

--noweb

at the end of the command line to get it to work without the phone home option.

[WonderingAtWork]

Thanks, unfortunately, that doesn't help me. I do want to connect to the web to use plink's annotation function (e.g. --lookup-gene).

[gringer]

can you connect to the web via other means (e.g. 'wget http://www.gringene.org')? I can't recall how plink connects to the web, but presumably if it can't do a version check then it also can't do the lookup-gene function.

[yl01]

Even if you have good internet connection, Plink's annotation function will not work. That function is relying on an external database and it has been not woking for at least two years.

[chrchang]

Even if you have good internet connection, Plink's annotation function will not work. That function is relying on an external database and it has been not woking for at least two years.

Indeed. You should use PLINK/SEQ for this function instead; the current plan is to drop it entirely from PLINK 1.9. (In the unlikely event that the PLINK/SEQ implementation is meaningfully worse for your application than what PLINK used to do, let me know and I'll look into the matter more closely.)

[WonderingAtWork]

Dear all, thanks a lot. Using PLINK/SEQ instead is a good idea.

[juanjingmiao]

PLINK : can be used on the other species?

does anyone have the experience of using Plink on the other species beside human? I don't find the limitation description about the PLINK. I want to obtain help. Thanks!

[chrchang]

PLINK 1.07 has limited support for nonhuman species via the --dog, --horse, --cow, --sheep, --rice, and --mouse flags; see http://pngu.mgh.harvard.edu/~purcell....shtml#species .

PLINK 1.9 is backwards-compatible with those flags, but also supports other user-defined chromosome sets with the --chr-set flag.

[juanjingmiao]

PLINK 1.07 has limited support for nonhuman species via the --dog, --horse, --cow, --sheep, --rice, and --mouse flags; see http://pngu.mgh.harvard.edu/~purcell....shtml#species .

PLINK 1.9 is backwards-compatible with those flags, but also supports other user-defined chromosome sets with the --chr-set flag.

Thank you very much!