Snippy-multi returns 0 SNPs while snippy finds multiple

[asad-869]

Hi everyone,

I am facing an issue while using snippy-multi. It returns 0 SNPs. I have tried one of my genome individually with the snippy command and it returns 22 SNPs. However, when I use the same file in .tab file and use the snippy-multi, it says no SNPs found. Moreover, the snippy returns 272700 sam records, while the snippy-multi returns only 350 sam records. Please help me