Failed to select autosomal SNPs only (QC Step 3)
Franklin593 opened this issue · comments
While running:
# Select autosomal SNPs only (i.e., from chromosomes 1 to 22).
awk '{ if ($1 >= 1 && $1 <= 22) print $2 }' HapMap_3_r3_6.bim > snp_1_22.txt
plink --bfile HapMap_3_r3_6 --extract snp_1_22.txt --make-bed --out HapMap_3_r3_7
Here are the error logs:
PLINK v1.90b7.2 64-bit (11 Dec 2023) www.cog-genomics.org/plink/1.9/
(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to HapMap_3_r3_7.log.
Options in effect:
--bfile HapMap_3_r3_6
--extract snp_1_22.txt
--make-bed
--out HapMap_3_r3_7
16125 MB RAM detected; reserving 8062 MB for main workspace.
1430443 variants loaded from .bim file.
165 people (81 males, 84 females) loaded from .fam.
112 phenotype values loaded from .fam.
Error: No variants remaining after --extract.
Here are the HapMap_3_r3_6.bim:
1 rs2185539 0 556738 T C
1 rs11240767 0 718814 T C
1 rs3131972 0 742584 A G
1 rs3131969 0 744045 A G
1 rs1048488 0 750775 C T
Here are the snp_1_22.txt
rs2185539
rs11240767
rs3131972
rs3131969
rs1048488
I have searched through Google and documents, but still haven't found a solution.
Your input or guidance on this would be highly appreciated