PLINK v1.9.0-b.7.11 64-bit (19 Aug 2025)
Options in effect:
  --make-bed
  --map /usr/local/data/cc.map
  --out cc.begin
  --ped /usr/local/data/cc.ped

Hostname: ip-10-0-202-29
Working directory: /home/elizabeth/Day2/GenotypeQC/QCdata
Start time: Tue Jun  2 06:17:56 2026

Random number seed: 1780402676
62946 MB RAM detected; reserving 31473 MB for main workspace.
Scanning .ped file... done.
Performing single-pass .bed write (484128 variants, 193 people).
--file: cc.begin-temporary.bed + cc.begin-temporary.bim +
cc.begin-temporary.fam written.
484128 variants loaded from .bim file.
193 people (107 males, 86 females) loaded from .fam.
193 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 193 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Warning: 2177 het. haploid genotypes present (see cc.begin.hh ); many commands
treat these as missing.
Total genotyping rate is 0.963235.
484128 variants and 193 people pass filters and QC.
Among remaining phenotypes, 127 are cases and 66 are controls.
--make-bed to cc.begin.bed + cc.begin.bim + cc.begin.fam ... done.

End time: Tue Jun  2 06:17:59 2026