Error: Please supply a reference FASTA/GBK/EMBL file with --reference , even in the presence of reference file

[neelam19051]

Hi, i am trying to run snippy on multiple genomes, however it gives following error like Please supply a reference FASTA/GBK/EMBL file with --reference even after providing the reference file. i don't understand why it is happen and here is code which i am using-

@ #

• [ ] > #!/bin/bash
• [ ] >
• [ ] > # specify the directory containing the genome files
• [ ] > genome_dir=/home/bvs/Neelam/fna
• [ ] >
• [ ] > # specify the reference genome
• [ ] > ref=/home/bvs/Neelam/ref_snippy/PAO1.fna
• [ ] >
• [ ] > # specify the directory for the output files
• [ ] > out_dir=/home/bvs/Neelam/snippy_outdir
• [ ] >
• [ ] > # specify the contigs files
• [ ] > #contig=/home/bvs/neelam/annotated/fna
• [ ] >
• [ ] >
• [ ] > # loop through all the genome files in the directory
• [ ] > for file in $(find $genome_dir -type f -name "*.fna"); do
• [ ] >
• [ ] > # extract the sample name from the file name
• [ ] > name=$(echo $file | cut -d"/" -f 2 | cut -d"." -f1)
• [ ] >
• [ ] > # run Snippy with the sample name as the prefix
• [ ] > snippy --prefix $name $file --cpus 30 --outdir $out_dir --reference $ref --ctgs $genome_dir
• [ ] >
• [ ] > done
• [ ] >
• [ ] >
• [ ] >
• [ ] >

This is snippy 4.6.0 [16:47:05] Written by Torsten Seemann [16:47:05] Obtained from https://github.com/tseemann/snippy [16:47:05] Detected operating system: linux [16:47:05] Enabling bundled linux tools. [16:47:05] Found bwa - /usr/bin/bwa [16:47:05] Found bcftools - /home/bvs/Neelam/snippy/binaries/linux/bcftools [16:47:05] Found samtools - /usr/bin/samtools [16:47:05] Found java - /usr/bin/java [16:47:05] Found snpEff - /home/bvs/Neelam/snippy/binaries/noarch/snpEff [16:47:05] Found samclip - /home/bvs/Neelam/snippy/binaries/noarch/samclip [16:47:05] Found seqtk - /usr/bin/seqtk [16:47:05] Found parallel - /usr/bin/parallel [16:47:05] Found freebayes - /home/bvs/Neelam/snippy/binaries/linux/freebayes [16:47:05] Found freebayes-parallel - /home/bvs/Neelam/snippy/binaries/noarch/freebayes-parallel [16:47:05] Found fasta_generate_regions.py - /home/bvs/Neelam/snippy/binaries/noarch/fasta_generate_regions.py [16:47:05] Found vcfstreamsort - /home/bvs/Neelam/snippy/binaries/linux/vcfstreamsort [16:47:05] Found vcfuniq - /home/bvs/Neelam/snippy/binaries/linux/vcfuniq [16:47:05] Found vcffirstheader - /home/bvs/Neelam/snippy/binaries/noarch/vcffirstheader [16:47:05] Found gzip - /usr/bin/gzip [16:47:05] Found vt - /home/bvs/Neelam/snippy/binaries/linux/vt [16:47:05] Found snippy-vcf_to_tab - /home/bvs/Neelam/snippy/bin/snippy-vcf_to_tab [16:47:05] Found snippy-vcf_report - /home/bvs/Neelam/snippy/bin/snippy-vcf_report [16:47:05] Checking version: samtools --version is >= 1.7 - ok, have 1.9 [16:47:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.10 [16:47:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.1 [16:47:06] Checking version: snpEff -version is >= 4.3 - ok, have 4.3 [16:47:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:47:06] Please supply a reference FASTA/GBK/EMBL file with --reference

Thank you!