Removing Duplicated Sample IDs
19 views
Skip to first unread message
Farnoosh Ghaffaran
Jun 20, 2025, 11:05:17 AM6/20/25
to plink2-users
How can I solve this?
PLINK v2.00a4.3 AVX2 (10 Jun 2023)
Options in effect:
--make-pgen
--out merged_chr1_22_no_dups
--pfile merged_chr1_22
--remove duplicate_ids.txt
...
Random number seed: 1750431667
257655 MiB RAM detected, ~227264 available; reserving 128827 MiB for main
workspace.
Using 1 compute thread.
2008 samples (0 females, 0 males, 2008 ambiguous; 2008 founders) loaded from
merged_chr1_22.psam.
422893758 variants loaded from merged_chr1_22.pvar.
Note: No phenotype data present.
Error: Duplicate ID '0 A1055'.
End time: Fri Jun 20 16:02:25 2025
PLINK v2.00a4.3 AVX2 (10 Jun 2023)
Options in effect:
--make-pgen
--out merged_chr1_22_no_dups
--pfile merged_chr1_22
--remove duplicate_ids.txt
...
Random number seed: 1750431667
257655 MiB RAM detected, ~227264 available; reserving 128827 MiB for main
workspace.
Using 1 compute thread.
2008 samples (0 females, 0 males, 2008 ambiguous; 2008 founders) loaded from
merged_chr1_22.psam.
422893758 variants loaded from merged_chr1_22.pvar.
Note: No phenotype data present.
Error: Duplicate ID '0 A1055'.
End time: Fri Jun 20 16:02:25 2025
Chris Chang
Jun 20, 2025, 11:40:20 AM6/20/25
to Farnoosh Ghaffaran, plink2-users
How was that invalid .psam file created?
You can either backtrack to that step and avoid creating an invalid .psam, or you can e.g. write a script to temporarily replace e.g. the first instance of "A1055" with "A1055_1", the second with "A1055_2", etc.
--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/plink2-users/9e73d1a5-b975-4caa-ae60-41307a9e8f96n%40googlegroups.com.
Reply all
Reply to author
Forward
0 new messages