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ld_qc.log
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ld_qc.log
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PLINK v1.90b7.1 64-bit (18 Oct 2023)
Options in effect:
--bfile qc
--indep-pairwise 50 5 0.2
--out ld_qc
Hostname: Alejandros-MacBook-Air.local
Working directory: /Users/efra/Documents/LCG/5th/Statistical Genetics/gh/StatisticalGenomics/Project
Start time: Tue Nov 14 21:08:57 2023
Random number seed: 1700017737
24576 MB RAM detected; reserving 12288 MB for main workspace.
382054 variants loaded from .bim file.
1375 people (920 males, 455 females) loaded from .fam.
1375 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1375 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.992056.
382054 variants and 1375 people pass filters and QC.
Among remaining phenotypes, 708 are cases and 667 are controls.
Pruned 23542 variants from chromosome 1, leaving 7490.
Pruned 25223 variants from chromosome 2, leaving 7316.
Pruned 20582 variants from chromosome 3, leaving 6310.
Pruned 18590 variants from chromosome 4, leaving 5786.
Pruned 19206 variants from chromosome 5, leaving 5963.
Pruned 18651 variants from chromosome 6, leaving 5631.
Pruned 15878 variants from chromosome 7, leaving 5144.
Pruned 16828 variants from chromosome 8, leaving 4826.
Pruned 13960 variants from chromosome 9, leaving 4427.
Pruned 16343 variants from chromosome 10, leaving 5084.
Pruned 14957 variants from chromosome 11, leaving 4527.
Pruned 13884 variants from chromosome 12, leaving 4765.
Pruned 11473 variants from chromosome 13, leaving 3672.
Pruned 9253 variants from chromosome 14, leaving 3210.
Pruned 8409 variants from chromosome 15, leaving 3033.
Pruned 8945 variants from chromosome 16, leaving 3246.
Pruned 6052 variants from chromosome 17, leaving 2741.
Pruned 8463 variants from chromosome 18, leaving 3026.
Pruned 3277 variants from chromosome 19, leaving 1808.
Pruned 7327 variants from chromosome 20, leaving 2767.
Pruned 4036 variants from chromosome 21, leaving 1501.
Pruned 3387 variants from chromosome 22, leaving 1515.
Pruning complete. 288266 of 382054 variants removed.
Marker lists written to ld_qc.prune.in and ld_qc.prune.out .
End time: Tue Nov 14 21:08:57 2023