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chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
https://www.cog-genomics.org/plink/2.0/
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0 phenotype values present after --pheno. #247

Closed lukaskon closed 1 year ago

lukaskon commented 1 year ago

Hello, I am stuck trying to figure out why the phenotypes are not recognized in my file below. I checked that the FID/IIDs match between my pheno file and .fam file, then checked that both files are delimited correctly, but not sure what to check next. Thanks in advance!

(base) Association_study$ head Crop_pheno
0 AI20 Poinsettia
0 AI7 Poinsettia
0 B15 Poinsettia
0 B6 Poinsettia
0 BF14 Geranium
0 BF27 Geranium
0 BF5 Geranium
0 BF9 Geranium
0 BG12 Geranium
0 BG18 Geranium
(base) Association_study$ head Bcin_GWAS_276_9.fam
0 AI20 0 0 0 -9
0 AI7 0 0 0 -9
0 B15 0 0 0 -9
0 B6 0 0 0 -9
0 BF14 0 0 0 -9
0 BF27 0 0 0 -9
0 BF5 0 0 0 -9
0 BF9 0 0 0 -9
0 BG12 0 0 0 -9
0 BG18 0 0 0 -9
(base) Association_study$ plink --bfile Bcin_GWAS_276_9 --allow-no-sex --assoc --pheno Crop_pheno --all-pheno --out Croponly4_GWAS_assoc_results
PLINK v1.90b6.6 64-bit (10 Oct 2018)           www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to Croponly4_GWAS_assoc_results.log.
Options in effect:
  --all-pheno
  --allow-no-sex
  --assoc
  --bfile Bcin_GWAS_276_9
  --out Croponly4_GWAS_assoc_results
  --pheno Crop_pheno

1031524 MB RAM detected; reserving 515762 MB for main workspace.
17122 variants loaded from .bim file.
276 people (0 males, 0 females, 276 ambiguous) loaded from .fam.
Ambiguous sex IDs written to Croponly4_GWAS_assoc_results.nosex .
0 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 276 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.994271.
17122 variants and 276 people pass filters and QC.
Note: No phenotypes present.
0 phenotype values present after --pheno.
chrchang commented 1 year ago

Please ask basic usage questions in the plink2-users Google group, not here.