K-mer association with mixed effects model

[komaltilwani53]

Hi Team,

Appreciate if someone can advise me on this issue:
Previous steps:

1. SNP and COG association with fixed effects model

Pyseer having issue: K-mer association with mixed effects model

Command used:
pyseer --lmm --phenotypes phenotypes.txt --kmers fsm_kmers.txt.gz --similarity phylogeny_K.tsv --output-patterns kmer_patterns.txt --cpu 12 > cdi_kmers.txt

Standard output: None

Standard Error file:
Read 602 phenotypes
Detected binary phenotype
Setting up LMM
Similarity matrix has dimension (602, 602)
Analysing 602 samples found in both phenotype and similarity matrix
h^2 = 0.00
No observations of TTTNNNNNN in selected samples
No observations of TTTNNNNNNN in selected samples
No observations of TTTNNNNNNNN in selected samples
No observations of TTTNNNNNNNNN in selected samples
No observations of TTTNNNNNNNNNN in selected samples
No observations of TTTNNNNNNNNNNN in selected samples
No observations of TTTNNNNNNNNNNNN in selected samples

Environment Verified and Test cases executed as shared in tutorial.

Please let me know in case if any further inputs required to investigate this issue

[johnlees]

Sorry I'm not clear from the above what is the issue you are having?