Error: --pheno: file does not exist

[Ioana Anghel]

Hello,

 

I am trying to run various commands in plink2 and having a strange error that the file I am referencing does not exist. This has happened with --pheno and --read-freq. I tried to specify the absolute path to the file and to regenerate the files, and I am still getting this error. Do you know what could be the issue? 

.plink2 --bfile 77-Linanthus_Transect2 --pheno transect2samples.txt --fst 3 report-variants --out Linanthus_Fst

PLINK v2.0.0-a.6.33 32-bit (28 Feb 2026)            cog-genomics.org/plink/2.0/

(C) 2005-2026 Shaun Purcell, Christopher Chang    GNU General Public License v3

Logging to Linanthus_Fst.log.

Options in effect:

  --bfile 77-Linanthus_Transect2

  --fst 3 report-variants

  --out Linanthus_Fst

  --pheno transect2samples.txt

Start time: Wed Mar 25 17:11:43 2026

Error: --pheno:

transect2samples.txt

does not exist..

Thank you,

Ioana

[Chris Chang]

1. Is there a reason you are using a 32-bit build?  A 64-bit build is almost always a better choice.

2. Please post the actual .log file (not copy-and-pasted, I need the raw bytes), along with the output of running “ls -al transect2samples.txt” immediately afterward.

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