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.

[LuXX6666]

Has the problem been solved? I want to know how to deal with it

[cpplyqz]

Has the problem been solved? I want to know how to deal with it I don't remember clearly, I installed a lower version of snippy

[xupanpan001]

Has the problem been solved? I want to know how to deal with it I don't remember clearly, I installed a lower version of snippy

Do you remember which vesion of snippy you finally install? thank you