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snippy -Loaded 1 sequences totalling 0 bp

Open hooohw opened this issue 1 year ago • 0 comments

hello,i have a question i cannot deal. here is my code: snippy-multi snp.txt --ref sequence.gb --cpus 40 > sy.sh sh sy.sh output: [11:08:18] Using read file: /home/data/zzz/China-pig-309/GCA_003310565.1_ASM331056v1_genomic.fasta [11:08:18] Output folder GCA_003310565.1_ASM331056v1_genomic already exists. Remove or use --force. [11:08:18] This is snippy 4.3.6 [11:08:18] Written by Torsten Seemann [11:08:18] Obtained from https://github.com/tseemann/snippy [11:08:18] Detected operating system: linux [11:08:18] Enabling bundled linux tools. [11:08:18] Found bwa - /home/anaconda/envs/snippy/bin/bwa [11:08:18] Found bcftools - /home/anaconda/envs/snippy/bin/bcftools [11:08:18] Found samtools - /home/anaconda/envs/snippy/bin/samtools [11:08:18] Found java - /home/anaconda/envs/snippy/bin/java [11:08:18] Found snpEff - /home/anaconda/envs/snippy/bin/snpEff [11:08:18] Found samclip - /home/anaconda/envs/snippy/bin/samclip [11:08:18] Found seqtk - /home/anaconda/envs/snippy/bin/seqtk [11:08:18] Found parallel - /home/anaconda/envs/snippy/bin/paralle ####repeat##### This is snippy-core 4.3.6 Obtained from http://github.com/tseemann/snippy Enabling bundled tools. Found any2fasta - /home/anaconda/envs/snippy/binaries/noarch/any2fasta Found samtools - /home/anaconda/envs/snippy/bin/samtools Found minimap2 - /home/anaconda/envs/snippy/bin/minimap2 Found bedtools - /home/anaconda/envs/snippy/bin/bedtools Found snp-sites - /home/anaconda/envs/snippy/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening 'GCA_003309105.1_ASM330910v1_genomic/ref.fa' Detected FASTA format Read 2 lines from 'GCA_003309105.1_ASM330910v1_genomic/ref.fa' Wrote 1 sequences from FASTA file. Processed 1 files. Done. Use of uninitialized value in uc at /home/anaconda/envs/snippy/bin/snippy-core line 392, <GEN0> line 1. Loaded 1 sequences totalling 0 bp. Illegal division by zero at /home/anaconda/envs/snippy/bin/snippy-core line 145.

can you teach me solve the problem Appreciate very much have a nice day

hooohw avatar Jun 28 '23 06:06 hooohw