Ncbi-amrfinderplus

Introduction

Ncbi-amrfinderplus and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa.

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/ncbi-amrfinderplus

Home page: https://github.com/ncbi/amr

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	3.10.30, 3.10.42, 3.11.2
BELL	3.10.30, 3.10.42, 3.11.2
GAUTSCHI	3.10.30, 3.10.42, 3.11.2
NEGISHI	3.10.30, 3.10.42, 3.11.2
SCHOLAR	3.10.30, 3.10.42, 3.11.2

Commands

• amrfinder

• amr_report

• amrfinder_update

Module

You can load the modules by:

module load biocontainers
module load ncbi-amrfinderplus

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run ncbi-amrfinderplus on our clusters:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ncbi-amrfinderplus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ncbi-amrfinderplus

# Your ncbi-amrfinderplus workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ncbi-amrfinderplus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ncbi-amrfinderplus

# Your ncbi-amrfinderplus workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ncbi-amrfinderplus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ncbi-amrfinderplus

# Your ncbi-amrfinderplus workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ncbi-amrfinderplus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ncbi-amrfinderplus

# Your ncbi-amrfinderplus workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ncbi-amrfinderplus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ncbi-amrfinderplus

# Your ncbi-amrfinderplus workflow...