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I installed PuTTYgen on Windows using: putty-64bit-0.79-installer.msi (which I downloaded from the official PuTTYgen website).

Except that when I go to Windows cmd and run puttygen -V, I get the error "Unrecognised option -V". What's worse is that this message is displayed regardless of the option entered.

I have to use PuTTYgen as a batch script without going through the interface to transform an id_rsa file into id_rsa.ppk.

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Windows PuTTYgen is mostly GUI only. It seems that you expect it to support the command-line options that Linux console puttygen does. It does not.

Instead, you can use WinSCP console, which supports some console puttygen functionality:

winscp.com /keygen id_rsa -o id_rsa.ppk

WinSCP does not support the -O switch, but the -O private is the default (and the only) conversion it supports.

(I'm the author of WinSCP)

For other options, see:
How do you convert an SSH private key to a .ppk on the Windows command line?

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