abnormal update failure in by using --update-map

[Nixon So]

Dear All, 

After I used liftOver to convert the SNP coordinates from hg19 to hg38, I tried to update all the bfile by running this code:
plink --bfile copy_ukb22418_c22_b0_v2 --update-map updated_positions.txt 1 2 --make-bed --out updated_prefix
PLINK v1.9.0-b.7.7 64-bit (22 Oct 2024)            cog-genomics.org/plink/1.9/
(C) 2005-2024 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to updated_prefix.log.
Options in effect:
  --bfile copy_ukb22418_c22_b0_v2
  --make-bed
  --out updated_prefix
  --update-map updated_positions.txt 1 2

56231 MB RAM detected; reserving 28115 MB for main workspace.
12968 variants loaded from .bim file.
488377 people (223321 males, 264581 females, 475 ambiguous) loaded from .fam.
Ambiguous sex IDs written to updated_prefix.nosex .
--update-map: 0 values updated, 12942 variant IDs not present.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 488377 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.972879.
12968 variants and 488377 people pass filters and QC.
Note: No phenotypes present.
--make-bed to updated_prefix.bed + updated_prefix.bim + updated_prefix.fam ...
done.

, but it returns a messages that --update-map: 0 values updated, 12942 variant IDs not present.

I already checked both files, here is the checking code and the results:
cat -A copy_ukb22418_c22_b0_v2.bim | head
22^Irs62224618^I0^I16057417^IC^IT$
22^IAffx-52233492^I0^I16287538^IG^IC$
22^Irs200923174^I0^I16287557^IC^IG$
22^IAffx-80289661^I0^I16287585^IAC^IA$
22^IAffx-80289662^I0^I16287663^ITC^IT$
22^IAffx-52336937^I0^I16287779^ICT^IC$
22^Irs138257042^I0^I16449075^IG^IA$
22^Irs116911124^I0^I16495833^IC^IA$
22^Irs117578132^I0^I16595552^IC^IA$
22^Irs117982183^I0^I16648658^IC^IT$

cat -A updated_positions.txt | head
rs62224618^I15920591$
Affx-52233492^I15690425$
rs200923174^I15690406$
Affx-80289661^I15690378$
Affx-80289662^I15690300$
Affx-52336937^I15690184$
rs138257042^I15528888$
rs116911124^I15482130$
rs117578132^I15382411$
rs117982183^I15329305$


, it seems they are both looking normal and do have matched SNP id, but what happened to the code ? Many Thanks. Have a nice day.

Yours sincerely,

Nixon So

[Chris Chang]

Look carefully at how —update-map’s second and third parameters are defined.

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