I’m running Snippy v4.6.0 on assembled Klebsiella pneumoniae genomes using a 5 Mb reference with ~95 % ANI to all isolates. Each individual Snippy run completes successfully and reports multiple variants (SNPs, insertions, deletions, etc.) in snps.tab and snps.vcf. However, when I run snippy-core --ref ../Reference_Genome.fna --prefix core_all */, the output shows “0 core SNPs,” and the core.summary file indicates 400 000–600 000 bp unaligned for every sample. Some isolates also lack a snps.consensus.fa file. I suspect this may be due to the reference being too distant, large unaligned regions, or possibly a filtering or vt normalization issue specific to Snippy 4.6.0. Has anyone encountered similar behavior or can suggest how to troubleshoot it? Would using paired-end reads instead of contigs or relaxing the core alignment filters help resolve this?

(Ubuntu 22.04, Snippy 4.6.0 via Conda)