How to interpret the warning message "WARNING: the maximum identity threshold is <0.99"

[alimayy]

Hi there,

Many thanks for your work on strainest. Could you give a short explanation on how to interpret the following warning message?

WARNING: the maximum identity threshold is <0.99 and StrainEst has inferred a mixture of strains. The mixture of strains could be a single strain with no available reference genome. Please check the file counts.txt.

In our case, we get this when we use strainest on a low-complexity community of a certain bacterial species (2-4 strains) where the strains are quite similar to each other in terms of their genomes sequences. We do have the genome sequences available which we use in the strainest analysis.

Thanks,
Ali