snippy core took isolate as ref

Question

snippy core took isolate as ref

tbazilegith opened this issue a year ago · 1 comments

tbazilegith commented a year ago

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

Answer 1 · 2023-10-19T14:55:23.000Z

Hi!
It is wrking fine. If you look closer, it is using the ref.fa file inside the isol19001326 directory. Every output directory stores the reference sequence (the one you specified) in that file.

Hope this helps.

Alejandro