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tseemann / snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment
GNU General Public License v2.0
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snippy-core --prefix #490

Open yustinus1 opened 2 years ago

yustinus1 commented 2 years ago

Hello Tseemann, I ran the script "snippy-core --prefix TB0065_S16_L001 TB0207_S6_L001" and I got the following error. Can you help me?

This is snippy-core 4.5.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools. Found any2fasta - /home/litbangkes-papua/anaconda3/envs/my_env/bin/any2fasta Found samtools - /home/litbangkes-papua/anaconda3/envs/my_env/bin/samtools Found minimap2 - /home/litbangkes-papua/anaconda3/envs/my_env/bin/minimap2 Found bedtools - /home/litbangkes-papua/anaconda3/envs/my_env/bin/bedtools Found snp-sites - /home/litbangkes-papua/anaconda3/envs/my_env/bin/snp-sites ERROR: Please provide --ref FASTA/GENBANK

qingbo11 commented 2 years ago

Please try this "snippy-core --ref YOUR REF SEQ FILE.gbk --prefix TB0065_S16_L001 TB0207_S6_L001"

yustinus1 commented 2 years ago

thank you Qingbo11 for your answer, I can solve this problem now. If I want to add an out group during the construction of the phylogenetic tree, how do I do it?

qingbo11 commented 2 years ago

Everyone who knows this better please correct me if I am wrong. My understanding is that the ref seq is used to align all seqs including your out group one. Therefore, maybe you want to try to add the out group one's seq during snippy-core analysis of core snps. It may have no SNPs detected from this out group one, but finally the tree may show this distant one as you need to get there to see what happen. Good luck!

yustinus1 commented 2 years ago

Thank you very much for your help.

neelam19051 commented 1 year ago

Hi, I have different strains file for example E.coli_AB311, E.coli_LE392 ; AG1 and so on. And I want my output file will created according to name of file. If anyone know anything please let me know.

Thank you!