No people remaining after --keep.

[jintong zhao]

Hi all, 

I was going to extract a subset of individuals. These are my command and log.

(base) MacBook-Air-2:plink_mac mac$ ./plink --file success.3 --keep patientID_GWAS.txt --make-bed --out success.4

PLINK v1.90p 64-bit (13 Feb 2023)            www.cog-genomics.org/plink/1.9/

(C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to success.4.log.

Options in effect:

  --file success.3

  --keep patientID_GWAS.txt

  --make-bed

  --out success.4

16384 MB RAM detected; reserving 8192 MB for main workspace.

Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.

.ped scan complete (for binary autoconversion).

Performing single-pass .bed write (660002 variants, 1629 people).

--file: success.4-temporary.bed + success.4-temporary.bim +

success.4-temporary.fam written.

660002 variants loaded from .bim file.

1629 people (0 males, 0 females, 1629 ambiguous) loaded from .fam.

Ambiguous sex IDs written to success.4.nosex .

Error: No people remaining after --keep.

(base) MacBook-Air-2:plink_mac mac$ head success.3.ped

203253090213 R01C01 0 0 0 -9 0 0 C C T T 0 0 G G A G G G 0 0 G G 0 0 0 0 T T A C T T T T C C 0 0 A A 0 0 A A T C T T C C C C G G ...

(base) MacBook-Air-2:plink_mac mac$ head filtered_ex.txt

203253090213 "R01C01"

203253090213 "R01C02"

203253090213 "R02C01"

203253090213 "R02C02"

203253090213 "R03C01"

203253090213 "R03C02"

203253090213 "R04C01"

203253090213 "R04C02"

203253090213 "R05C01"

203253090213 "R05C02"

I was fighting all day and looked through almost all relevant website but still confused😭

[Christopher Chang]

Look carefully at the IDs in the .ped file, and the IDs in the --keep file.  Can you find something that's different between them?

[cls]

Please may I check if this has been resolved?

I've recently been receiving this error too and can't seem to resolve it (tried --keep file with only IID; IID and FID, header and without). I've checked the IIDs and I can't see any differences between them.