.gb file not working as the reference and with fasta reference, FTYPE,STRAND,NT_POS, AA_POS , EFFECT,LOCUS_TAG,GENE PRODUCT are empty columns

[absartalat]

I installed snippy v 4.6.0 and snpEff version SnpEff 5.1d (build 2022-04-19 15:49). When the reference file is a .gb file, I encounter the following error [19:30:07] This is snippy 4.6.0 [19:30:07] Written by Torsten Seemann [19:30:07] Obtained from https://github.com/tseemann/snippy [19:30:07] Detected operating system: linux [19:30:07] Enabling bundled linux tools. [19:30:07] Found bwa - /home/absar_ubuntu/anaconda3/envs/snippy/bin/bwa [19:30:07] Found bcftools - /home/absar_ubuntu/anaconda3/envs/snippy/bin/bcftools [19:30:07] Found samtools - /home/absar_ubuntu/anaconda3/envs/snippy/bin/samtools [19:30:07] Found java - /home/absar_ubuntu/anaconda3/envs/snippy/bin/java [19:30:07] Found snpEff - /home/absar_ubuntu/anaconda3/envs/snippy/bin/snpEff [19:30:07] Found samclip - /home/absar_ubuntu/anaconda3/envs/snippy/bin/samclip [19:30:07] Found seqtk - /home/absar_ubuntu/anaconda3/envs/snippy/bin/seqtk [19:30:07] Found parallel - /home/absar_ubuntu/anaconda3/envs/snippy/bin/parallel [19:30:07] Found freebayes - /home/absar_ubuntu/anaconda3/envs/snippy/bin/freebayes [19:30:07] Found freebayes-parallel - /home/absar_ubuntu/anaconda3/envs/snippy/bin/freebayes-parallel [19:30:07] Found fasta_generate_regions.py - /home/absar_ubuntu/anaconda3/envs/snippy/bin/fasta_generate_regions.py [19:30:07] Found vcfstreamsort - /home/absar_ubuntu/anaconda3/envs/snippy/bin/vcfstreamsort [19:30:07] Found vcfuniq - /home/absar_ubuntu/anaconda3/envs/snippy/bin/vcfuniq [19:30:07] Found vcffirstheader - /home/absar_ubuntu/anaconda3/envs/snippy/bin/vcffirstheader [19:30:07] Found gzip - /usr/bin/gzip [19:30:07] Found vt - /home/absar_ubuntu/anaconda3/envs/snippy/bin/vt [19:30:07] Found snippy-vcf_to_tab - /home/absar_ubuntu/anaconda3/envs/snippy/bin/snippy-vcf_to_tab [19:30:07] Found snippy-vcf_report - /home/absar_ubuntu/anaconda3/envs/snippy/bin/snippy-vcf_report [19:30:07] Checking version: samtools --version is >= 1.7 - ok, have 1.16 [19:30:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.16 [19:30:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6 [19:30:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.1 [19:30:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:30:07] Using reference: /home/absar_ubuntu/NZ_CP042858.1.gb [19:30:07] Treating reference as 'genbank' format. [19:30:07] Will use 4 CPU cores. [19:30:07] Using read file: /home/absar_ubuntu/WGS_fasta/1.fna [19:30:07] Used --force, will overwrite existing SNP_rough1 [19:30:07] Changing working directory: SNP_rough1 [19:30:07] Creating reference folder: reference [19:30:07] Extracting FASTA and GFF from reference. [19:30:11] Wrote 1 sequences to ref.fa [19:30:11] Wrote 5799 features to ref.gff [19:30:11] Shredding /home/absar_ubuntu/WGS_fasta/1.fna into pseudo-reads [19:30:14] Wrote 466874 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [19:30:14] Creating reference/snpeff.config [19:30:14] Freebayes will process 7 chunks of 842934 bp, 4 chunks at a time. [19:30:14] Using BAM RG (Read Group) ID: SNP_rough1 [19:30:14] Running: samtools faidx reference/ref.fa 2>> snps.log [19:30:14] Running: bwa index reference/ref.fa 2>> snps.log [19:30:16] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [19:30:16] Running: ln -sf reference/ref.fa . 2>> snps.log [19:30:16] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [19:30:16] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [19:30:16] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [19:30:21] Error running command, check SNP_rough1/snps.log

Using .fasta file as reference gives empty column in the result.

[famiji]

i also meet this problem,is there anyway to solve it?if is, please let me know.

[absartalat]

@famiji When you download the GenBank version of the reference file from NCBI, select 'show GI' option too. That solved the error. Hope this helps!

[absartalat]

i also meet this problem,is there anyway to solve it?if is, please let me know.

@famiji You can try downgrading the snpeff version to 5.0 if still getting the problem. Check snpeff version first using snpEff -version If it's 5.1d, there is some incompatibility issues with snippy 4.6.0. Downgrade snpeff to 5.0, that worked for me. Command: conda activate Environment_name conda install snpeff=5.0 Hope this solves your issue.

[stanikae]

i also meet this problem,is there anyway to solve it?if is, please let me know.

@famiji You can try downgrading the snpeff version to 5.0 if still getting the problem. Check snpeff version first using snpEff -version If it's 5.1d, there is some incompatibility issues with snippy 4.6.0. Downgrade snpeff to 5.0, that worked for me. Command: conda activate Environment_name conda install snpeff=5.0 Hope this solves your issue.

This solution worked for me but might be necessary to include the channel when downgrading to v5.0: conda install -c bioconda snpeff=5.0