Subject: Issue running --pmerge on Windows 10 with PLINK2 alpha build

[Angela Flying]

I am encountering an issue running PLINK2 on Windows 10 while attempting to merge my sample with the 1000 Genomes PLINK1 dataset.

Environment:

• OS: Windows 10, 64-bit, x64-based processor

• Device Name: DESKTOP-OQTE0UM

• CPU: Intel(R) Core(TM) i5-7600 CPU @ 3.50GHz

• RAM: 16 GB

• Storage: 932 GB HDD + 238 GB SSD

• Graphics: NVIDIA GeForce GTX 1050 Ti (4 GB)

• PLINK2 version: v2.0.0-a.6.25 64-bit (alpha/development build, 19 Oct 2025)

• The executable previously worked for simple commands such as --version and --bfile.

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Commands attempted and errors:

1. CMD (Command Prompt):

D:\DNA>"D:\PLINK2\plink2.exe" --bfile "D:\DNA\1000G_autosomes" --pmerge "D:\DNA\my_sample" --make-bed --set-all-var-ids @:#:$r --out "D:\DNA\merged_final"

Error in CMD:

The specified executable is not a valid application for this OS platform.

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2. PowerShell:

& "D:\PLINK2\plink2.exe" --bfile "D:\DNA\1000G_autosomes" --pmerge "D:\DNA\my_sample" --make-bed --set-all-var-ids @:#:$r --out "D:\DNA\merged_final"

Error in PowerShell:

Program 'plink2.exe' failed to run: The specified executable is not a valid application for this OS platform. At line:1 char:1 + & "D:\PLINK2\plink2.exe" --bfile "D:\DNA\1000G_autosomes" ... + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CategoryInfo : ResourceUnavailable: (:) [], ApplicationFailedException + FullyQualifiedErrorId : NativeCommandFailed

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GPT intuition:
The executable runs simple commands without error, but fails on --pmerge. This suggests that the alpha/development build may not fully support complex merge routines on Windows 10, even though it is 64-bit.

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Request:
Could you confirm whether:

1. There is a stable Windows 64-bit build that fully supports --pmerge.

2. This is a known issue with the alpha build on Windows.

Thank you very much for your time and assistance!

[Chris Chang]

This OS error message has nothing to do with —pmerge.

Please spell out EXACTLY how the SAME executable DID work for —version and —bfile before it failed here.

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