no. variants normalized

[cpplyqz]

I use snippy 4.6.0 to calling my bacteria snp,but there are no result ,I wonder what to do next ,thanks.
snippy --outdir 135080RSH2439 --ref 175001_wt/175001R1qc_shovill.fasta --ctgs 135080RSH2439.fasta
[21:19:19] This is snippy 4.6.0
[21:19:19] Written by Torsten Seemann
[21:19:19] Obtained from https://github.com/tseemann/snippy
[21:19:19] Detected operating system: linux
[21:19:19] Enabling bundled linux tools.
[21:19:19] Found bwa - /home/lj_cpp/miniconda3/bin/bwa
[21:19:19] Found bcftools - /home/lj_cpp/miniconda3/bin/bcftools
[21:19:19] Found samtools - /home/lj_cpp/miniconda3/bin/samtools
[21:19:19] Found java - /home/lj_cpp/miniconda3/bin/java
[21:19:19] Found snpEff - /home/lj_cpp/miniconda3/bin/snpEff
[21:19:19] Found samclip - /home/lj_cpp/miniconda3/bin/samclip
[21:19:19] Found seqtk - /home/lj_cpp/miniconda3/bin/seqtk
[21:19:19] Found parallel - /home/lj_cpp/miniconda3/bin/parallel
[21:19:19] Found freebayes - /home/lj_cpp/miniconda3/bin/freebayes
[21:19:19] Found freebayes-parallel - /home/lj_cpp/miniconda3/bin/freebayes-parallel
[21:19:19] Found fasta_generate_regions.py - /home/lj_cpp/miniconda3/bin/fasta_generate_regions.py
[21:19:19] Found vcfstreamsort - /home/lj_cpp/miniconda3/bin/vcfstreamsort
[21:19:19] Found vcfuniq - /home/lj_cpp/miniconda3/bin/vcfuniq
[21:19:19] Found vcffirstheader - /home/lj_cpp/miniconda3/bin/vcffirstheader
[21:19:19] Found gzip - /usr/bin/gzip
[21:19:19] Found vt - /home/lj_cpp/miniconda3/bin/vt
[21:19:19] Found snippy-vcf_to_tab - /home/lj_cpp/miniconda3/bin/snippy-vcf_to_tab
[21:19:19] Found snippy-vcf_report - /home/lj_cpp/miniconda3/bin/snippy-vcf_report
[21:19:19] Checking version: samtools --version is >= 1.7 - ok, have 1.17
[21:19:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.17
[21:19:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6
[21:19:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.1
[21:19:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:19:20] Using reference: /home/lj_cpp/data/bacterial/175001_wt/175001R1qc_shovill.fasta
[21:19:20] Treating reference as 'fasta' format.
[21:19:20] Will use 8 CPU cores.
[21:19:20] Using read file: /home/lj_cpp/data/bacterial/snippy_result/135080RSH2439.fasta
[21:19:20] Creating folder: 135080RSH2439
[21:19:20] Changing working directory: 135080RSH2439
[21:19:20] Creating reference folder: reference
[21:19:20] Extracting FASTA and GFF from reference.
[21:19:20] Wrote 1 sequences to ref.fa
[21:19:20] Wrote 0 features to ref.gff
[21:19:20] Shredding /home/lj_cpp/data/bacterial/snippy_result/135080RSH2439.fasta into pseudo-reads
[21:19:26] Wrote 464230 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[21:19:26] Freebayes will process 15 chunks of 10770 bp, 8 chunks at a time.
[21:19:26] Using BAM RG (Read Group) ID: 135080RSH2439
[21:19:26] Running: samtools faidx reference/ref.fa 2>> snps.log
[21:19:26] Running: bwa index reference/ref.fa 2>> snps.log
[21:19:27] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[21:19:27] Running: ln -sf reference/ref.fa . 2>> snps.log
[21:19:27] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[21:19:27] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[21:19:27] Running: bwa mem -Y -M -R '@rg\tID:135080RSH2439\tSM:135080RSH2439' -t 8 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /tmp --threads 3 -m 2000M | samtools markdup -T /tmp --threads 3 -r -s - - > snps.bam 2>> snps.log
samtools: /home/lj_cpp/miniconda3/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
[M::bwa_idx_load_from_disk] read 0 ALT contigs
samtools: /home/lj_cpp/miniconda3/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::process] read 320000 sequences (80000000 bp)...
[M::process] read 144230 sequences (36042376 bp)...
[M::mem_process_seqs] Processed 320000 reads in 54.641 CPU sec, 10.488 real sec
[samclip] Processed 100000 records...
[samclip] Processed 200000 records...
[M::mem_process_seqs] Processed 144230 reads in 30.053 CPU sec, 4.559 real sec
[samclip] Processed 300000 records...
[samclip] Processed 400000 records...
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -Y -M -R @rg\tID:135080RSH2439\tSM:135080RSH2439 -t 8 reference/ref.fa fake_reads.fq
[main] Real time: 18.439 sec; CPU: 85.693 sec
[samclip] Total SAM records 464230, removed 71, allowed 0, passed 464159
[samclip] Header contained 3 lines
[samclip] Done.
[bam_sort_core] merging from 0 files and 3 in-memory blocks...
[bam_sort_core] merging from 0 files and 3 in-memory blocks...
[21:19:54] Running: samtools index snps.bam 2>> snps.log
[21:19:55] Running: fasta_generate_regions.py reference/ref.fa.fai 10770 > reference/ref.txt 2>> snps.log
[21:19:55] Running: freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
[21:19:55] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
normalize v0.5

options: input VCF file -
[o] output VCF file -
[w] sorting window size 10000
[n] no fail on reference inconsistency for non SNPs false
[q] quiet false
[d] debug false
[r] reference FASTA file reference/ref.fa

stats: biallelic
no. left trimmed : 0
no. right trimmed : 0
no. left and right trimmed : 0
no. right trimmed and left aligned : 0
no. left aligned : 0

total no. biallelic normalized : 0

multiallelic
no. left trimmed : 0
no. right trimmed : 0
no. left and right trimmed : 0
no. right trimmed and left aligned : 0
no. left aligned : 0

total no. multiallelic normalized : 0

total no. variants normalized : 0
total no. variants observed : 0
total no. reference observed : 0
Time elapsed: 0.00s

[21:19:55] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[21:19:55] Running: /home/lj_cpp/miniconda3/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[21:19:56] Running: /home/lj_cpp/miniconda3/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[21:19:56] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[21:19:56] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[21:19:56] Running: bcftools consensus --sample 135080RSH2439 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[21:19:56] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[21:19:56] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[21:19:56] Running: bcftools consensus --sample 135080RSH2439 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[21:19:56] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[21:19:56] Running: rm -f fake_reads.fq 2>> snps.log
[21:19:56] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
samtools: /home/lj_cpp/miniconda3/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /home/lj_cpp/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
[21:19:57] Marked 0 heterozygous sites with 'n'
[21:19:57] Creating extra output files: BED GFF CSV TXT HTML
[21:19:57] Identified 0 variants.
[21:19:57] Result folder: 135080RSH2439
[21:19:57] Result files:
[21:19:57] * 135080RSH2439/snps.aligned.fa
[21:19:57] * 135080RSH2439/snps.bam
[21:19:57] * 135080RSH2439/snps.bam.bai
[21:19:57] * 135080RSH2439/snps.bed
[21:19:57] * 135080RSH2439/snps.consensus.fa
[21:19:57] * 135080RSH2439/snps.consensus.subs.fa
[21:19:57] * 135080RSH2439/snps.csv
[21:19:57] * 135080RSH2439/snps.filt.vcf
[21:19:57] * 135080RSH2439/snps.gff
[21:19:57] * 135080RSH2439/snps.html
[21:19:57] * 135080RSH2439/snps.log
[21:19:57] * 135080RSH2439/snps.raw.vcf
[21:19:57] * 135080RSH2439/snps.subs.vcf
[21:19:57] * 135080RSH2439/snps.tab
[21:19:57] * 135080RSH2439/snps.txt
[21:19:57] * 135080RSH2439/snps.vcf
[21:19:57] * 135080RSH2439/snps.vcf.gz
[21:19:57] * 135080RSH2439/snps.vcf.gz.csi
[21:19:57] Walltime used: 38 seconds
[21:19:57] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues
[21:19:57] Done.