How to correct the long variants ID error?

Question

[bastemku]

I'm trying to join multiple imputed plinks files after removing duplicates to make a single file (plink1.bim, plink1.bed, plink1.fam) including all chromosomes. But I'm getting this error

>>>>Allocated 9000 MB successfully, after larger attempt(s) failed.
Warning: Unusually long variant ID(s) present.  PLINK 1.9 does not scale well
to length-80+ variant IDs; consider using a different naming scheme for long
indels and the like.
Error: Out of memory.  The --memory flag may be helpful.
Failed allocation size: 3212817216
5:38

How to correct the long variants ID error?

Thanks a lot for your assistance

Answer 1

[chrchang523]

Use plink 2.0 --set-all-var-ids to set shorter variant IDs before trying to use plink 1.9 on this dataset again.

[bastemku]

Thank you very much, it worked