plink1.9 --bfile phe.gen.data --score summary.stats.gz 1 2 3 header --q-score-range pvalue.threshold snp.pvals --extract ID.valid.snp --out PRS

That's the abbreviated summary stats (decompressed):

CHROM:POS37     ALT     BETA
10:100000625    G       0.017931
10:100000645    C       0.0065591
10:100002464    C       0.16826
10:100003242    G       0.016455

bim file:

1       1:752566        0       752566  G       A
1       1:752721        0       752721  A       G
1       1:754503        0       754503  G       A
1       1:798959        0       798959  A       G

And again, the same error: Error: Line 3 of --score file has fewer tokens than expected.

The summary stats and bim have the same variants and format. There are no missing values. I have no clue what's wrong.

Thanks.

* Update* You were correct. It worked when I used the decompressed file.