Error: Please supply a reference FASTA/GBK/EMBL file with --reference

Question

[Neel]

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!

Answer 1

[colindaven]

Type

echo $ref

to see if your ref has been saved in an environment variable. If this is empty it is a problem.

Else reenter your line, then retry

ref=/home/bvs/Neelam/ref_snippy/PAO1.fna

[Neel]

Yeah, its working now thank you so much for your reply.