snippy snippy core took isolate as ref

snippy core took isolate as ref

Open tbazilegith opened this issue 10 months ago • 1 comments

Hi Seeman I ran snippy on mutliple isolates with the input.tab

snippy-multi input.tab --ref ../gubbins_dir/ref_seq_dir/GCF_001600975_1_ASM160097v1.fasta --cpus 16 > runme.sh

When checked the file runme.sh, I noticed one of my isolates written as ref.

snippy-core --ref 'isol19001326/ref.fa' isol19001326 ...

Any idea? Should the reference sequence be in the input.tab as well? Thanks, TJ

Sep 03 '23 21:09 tbazilegith