Hello, I am trying to learn how to use nullarbor and I am getting and error
[11:06:59] Hello dn927558
[11:06:59] This is nullarbor.pl 2.0.20191013
[11:06:59] Send complaints to Torsten Seemann
[11:06:59] ERROR: Can not read reference 'NZ_CP012480.1.fna'
This is the reference number for Agalactiae which I found on the NCBI database.
Studying the Streptococcus Agalactiae fastq files I have compiled this error is coming up.
!/usr/bin/sh
SBATCH -n 1
SBATCH --cpus-per-task=24
SBATCH --mem=160000 # memory pool for all cores, this is in mb
Hello, I am trying to learn how to use nullarbor and I am getting and error [11:06:59] Hello dn927558 [11:06:59] This is nullarbor.pl 2.0.20191013 [11:06:59] Send complaints to Torsten Seemann [11:06:59] ERROR: Can not read reference 'NZ_CP012480.1.fna'
This is the reference number for Agalactiae which I found on the NCBI database. Studying the Streptococcus Agalactiae fastq files I have compiled this error is coming up.
!/usr/bin/sh
SBATCH -n 1
SBATCH --cpus-per-task=24
SBATCH --mem=160000 # memory pool for all cores, this is in mb
SBATCH -o /network/rit/lab/andamlab/Dowd/Vet_strep_Agalactiae/nullarbor_Agalactiae/nullarbor.slurm.%N.%j.out # STDOUT
SBATCH -D /network/rit/lab/andamlab/Dowd/Vet_strep_Agalactiae/nullarbor_Agalactiae # working directory
SBATCH --partition=batch
SBATCH -v
Activate the appropriate environment
source /network/rit/lab/andamlab/bin/miniconda3/etc/profile.d/conda.sh conda activate nullarbor umask g+rwx nullarbor.pl --name PROJAgalactia --mlst Streptococcus --ref NZ_CP012480.1.fna --input sample.tab --outdir OUTDIR exit 0
Is there something I am missing or is there somewhere else I could use a reference number?
Thank you, Dowd Naik