I'm trying to run snippy-multi for a few assembled genomes. 73 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/73.fasta 75 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/75.fasta 95 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/95.fasta A1 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/A1.fasta A6 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/A6.fasta D-3-11 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/D-3-11.fasta snippy-multi input.tab --reference Reference.gbk > 1.sh ./1.sh
The final result. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /root/miniconda3/envs/snippy/bin/any2fasta Found samtools - /root/miniconda3/envs/snippy/bin/samtools Found minimap2 - /root/miniconda3/envs/snippy/bin/minimap2 Found bedtools - /root/miniconda3/envs/snippy/bin/bedtools Found snp-sites - /root/miniconda3/envs/snippy/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening '73/ref.fa' Detected FASTA format Read 27360 lines from '73/ref.fa' Wrote 1 sequences from FASTA file. Processed 1 files. Done. Loaded 1 sequences totalling 1641481 bp. Will mask 0 regions totalling 0 bp ~ 0.00% ERROR: Could not find .aligned.fa/.vcf in 73
Viewed the log results in each file showing WARNING_GENE_NOT_FOUND: Too many 'WARNING_GENE_NOT_FOUND' warnings, no further warnings will be shown. WARNING_FRAMES_ZERO: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate. ERROR: CDS check file '/xulie/shiyanshijiyuanfenxi/jiyuanxulie/73/reference/./ref/cds.fa' not found. ERROR: Protein check file '/xulie/shiyanshijiyuanfenxi/jiyuanxulie/73/reference/./ref/protein.fa' not found. ERROR: Database check failed.
I don't know what to do can you help me
cross-posted https://github.com/tseemann/snippy/issues/506