--Genome returns empty output

[Khadija Sana]

Hi! 
I am trying to calculate the relatedness for a group of samples using --genome with a pihat threshold of 0.2. I expected to obtain a file with IBS calculation for each sample in the plink.genome file, however it returns an empty .genome file with just the header. 

Prior to using --genome I have filtered for MAF and also performed LD pruning. 

My log file looks like this:

PLINK v1.90b6.24 64-bit (6 Jun 2021)
Options in effect:
  --bfile Eur_0.05geno_mind_maf_hwe2_het
  --extract Eur_0.05geno_mind_maf_hwe2_indepSNP.prune.in
  --genome
  --min 0.2
  --out Eur_0.05geno_mind_maf_hwe2_het_pihat0.2

Random number seed: 1689347606
128677 MB RAM detected; reserving 64338 MB for main workspace.
277840 variants loaded from .bim file.
111 people (66 males, 45 females) loaded from .fam.
--extract: 92784 variants remaining.
Using up to 23 threads (change this with --threads).
Before main variant filters, 111 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.999006.
92784 variants and 111 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing Eur_0.05geno_mind_maf_hwe2_het_pihat0.2.genome .

The output s an empty file with just the headers:

 FID1                 IID1 FID2                 IID2 RT    EZ      Z0      Z1      Z2  PI_HAT PHE       DST     PPC   RATIO

Can anyone suggest what's going on?

Thanks in advance!

[Christopher Chang]

Think about what the --min flag does.

[Khadija Sana]

Right. There is no relatedness with the Pi_HAT threshold I provided and --min removes lines with PI_HAT values below the threshold. Makes sense, I overlooked that part. Running --genome without setting any parameter gives me the IBS calculation for each sample. 

Thanks