Hello, I'm testing the use of this software to identify some variants in my genomes (in FASTA format). When I use a FASTA file as the reference, everything works normally, but I do not have the gene information that I need. However, when I use a file in GBK format, I get the following error:
[11:07:40] This is snippy 4.4.0
[11:07:40] Written by Torsten Seemann
[11:07:40] Obtained from https://github.com/tseemann/snippy
[11:07:40] Detected operating system: linux
[11:07:40] Enabling bundled linux tools.
[11:07:40] Found bwa - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/bwa
[11:07:40] Found bcftools - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/bcftools
[11:07:40] Found samtools - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/samtools
[11:07:40] Found java - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/java
[11:07:40] Found snpEff - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/snpEff
[11:07:40] Found samclip - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/samclip
[11:07:40] Found seqtk - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/seqtk
[11:07:40] Found parallel - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/parallel
[11:07:40] Found freebayes - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/freebayes
[11:07:40] Found freebayes-parallel - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/freebayes-parallel
[11:07:40] Found fasta_generate_regions.py - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/fasta_generate_regions.py
[11:07:40] Found vcfstreamsort - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vcfstreamsort
[11:07:40] Found vcfuniq - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vcfuniq
[11:07:40] Found vcffirstheader - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vcffirstheader
[11:07:40] Found gzip - /usr/bin/gzip
[11:07:40] Found vt - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vt
[11:07:40] Found snippy-vcf_to_tab - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/snippy-vcf_to_tab
[11:07:40] Found snippy-vcf_report - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/snippy-vcf_report
[11:07:40] Checking version: samtools --version is >= 1.7 - ok, have 1.9
[11:07:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.9
[11:07:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3
[11:07:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.1
[11:07:41] Using reference: /mnt/c/Users/DAP/Desktop/snippy/cleaned_reference.gbk
[11:07:41] Treating reference as 'genbank' format.
[11:07:41] Will use 8 CPU cores.
[11:07:41] Using read file: /mnt/c/Users/DAP/Desktop/snippy/gv88.fasta
[11:07:41] Creating folder: /mnt/c/Users/DAP/Desktop/snippy/limpou
[11:07:41] Changing working directory: /mnt/c/Users/DAP/Desktop/snippy/limpou
[11:07:41] Creating reference folder: reference
[11:07:41] Extracting FASTA and GFF from reference.
[11:07:42] Wrote 1 sequences to ref.fa
[11:07:42] Wrote 2844 features to ref.gff
[11:07:42] Shredding /mnt/c/Users/DAP/Desktop/snippy/gv88.fasta into pseudo-reads
[11:07:46] Wrote 239084 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[11:07:46] Creating reference/snpeff.config
[11:07:46] Freebayes will process 15 chunks of 191231 bp, 8 chunks at a time.
[11:07:46] Using BAM RG (Read Group) ID: limpou
[11:07:46] Running: samtools faidx reference/ref.fa 2>> snps.log
[11:07:46] Running: bwa index reference/ref.fa 2>> snps.log
[11:07:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[11:07:47] Running: ln -sf reference/ref.fa . 2>> snps.log
[11:07:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[11:07:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[11:07:47] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[11:07:51] Error running command, check /mnt/c/Users/DAP/Desktop/snippy/limpou/snps.log
I've already grepped the reference, reinstalled other versions of Snippy, tried different references, and nothing seems to work.
Hello, I'm testing the use of this software to identify some variants in my genomes (in FASTA format). When I use a FASTA file as the reference, everything works normally, but I do not have the gene information that I need. However, when I use a file in GBK format, I get the following error:
[11:07:40] This is snippy 4.4.0
[11:07:40] Written by Torsten Seemann
[11:07:40] Obtained from https://github.com/tseemann/snippy
[11:07:40] Detected operating system: linux
[11:07:40] Enabling bundled linux tools.
[11:07:40] Found bwa - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/bwa
[11:07:40] Found bcftools - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/bcftools
[11:07:40] Found samtools - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/samtools
[11:07:40] Found java - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/java
[11:07:40] Found snpEff - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/snpEff
[11:07:40] Found samclip - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/samclip
[11:07:40] Found seqtk - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/seqtk
[11:07:40] Found parallel - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/parallel
[11:07:40] Found freebayes - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/freebayes
[11:07:40] Found freebayes-parallel - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/freebayes-parallel
[11:07:40] Found fasta_generate_regions.py - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/fasta_generate_regions.py
[11:07:40] Found vcfstreamsort - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vcfstreamsort
[11:07:40] Found vcfuniq - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vcfuniq
[11:07:40] Found vcffirstheader - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vcffirstheader
[11:07:40] Found gzip - /usr/bin/gzip
[11:07:40] Found vt - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/vt
[11:07:40] Found snippy-vcf_to_tab - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/snippy-vcf_to_tab
[11:07:40] Found snippy-vcf_report - /home/lmmbioinfo/miniconda3/envs/raelsnippy/bin/snippy-vcf_report
[11:07:40] Checking version: samtools --version is >= 1.7 - ok, have 1.9
[11:07:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.9
[11:07:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3
[11:07:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.1
[11:07:41] Using reference: /mnt/c/Users/DAP/Desktop/snippy/cleaned_reference.gbk
[11:07:41] Treating reference as 'genbank' format.
[11:07:41] Will use 8 CPU cores.
[11:07:41] Using read file: /mnt/c/Users/DAP/Desktop/snippy/gv88.fasta
[11:07:41] Creating folder: /mnt/c/Users/DAP/Desktop/snippy/limpou
[11:07:41] Changing working directory: /mnt/c/Users/DAP/Desktop/snippy/limpou
[11:07:41] Creating reference folder: reference
[11:07:41] Extracting FASTA and GFF from reference.
[11:07:42] Wrote 1 sequences to ref.fa
[11:07:42] Wrote 2844 features to ref.gff
[11:07:42] Shredding /mnt/c/Users/DAP/Desktop/snippy/gv88.fasta into pseudo-reads
[11:07:46] Wrote 239084 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[11:07:46] Creating reference/snpeff.config
[11:07:46] Freebayes will process 15 chunks of 191231 bp, 8 chunks at a time.
[11:07:46] Using BAM RG (Read Group) ID: limpou
[11:07:46] Running: samtools faidx reference/ref.fa 2>> snps.log
[11:07:46] Running: bwa index reference/ref.fa 2>> snps.log
[11:07:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[11:07:47] Running: ln -sf reference/ref.fa . 2>> snps.log
[11:07:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[11:07:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[11:07:47] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[11:07:51] Error running command, check /mnt/c/Users/DAP/Desktop/snippy/limpou/snps.log
I've already grepped the reference, reinstalled other versions of Snippy, tried different references, and nothing seems to work.