AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

References:

• Michael F. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021 Jun 16;11(1):12728.
• Michael F. Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob Agents Chemother. 2019 Oct 22;63(11):e00483-19..

• amr Main Site

• Module Name: amr (see the modules page for more information)
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • amr_HOME
• Example files in /usr/local/apps/amr/test_data
• Reference data in /usr/local/apps/amr/database

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive -c 4 --mem=10G --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load amr
[user@cn3144 ~]$ export $TMPDIR=/lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ amrfinder --help 
Identify AMR and virulence genes in proteins and/or contigs and print a report

DOCUMENTATION
    See https://github.com/ncbi/amr/wiki for full documentation

UPDATES
    Subscribe to the amrfinder-announce mailing list for database and software update notifications:
    https://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce

USAGE:   amrfinder [--update] [--force_update] [--protein PROT_FASTA] [--nucleotide NUC_FASTA] [--gff GFF_FILE] [--annotation_format ANNOTATION_FORMAT] [--database DATABASE_DIR] [--database_version] [--ident_min MIN_IDENT] [--coverage_min MIN_COV] [--organism ORGANISM] [--list_organisms] [--translation_table TRANSLATION_TABLE] [--plus] [--report_common] [--report_all_equal] [--name NAME] [--print_node] [--mutation_all MUT_ALL_FILE] [--output OUTPUT_FILE] [--protein_output PROT_FASTA_OUT] [--nucleotide_output NUC_FASTA_OUT] [--nucleotide_flank5_output NUC_FLANK5_FASTA_OUT] [--nucleotide_flank5_size NUC_FLANK5_SIZE] [--blast_bin BLAST_DIR] [--hmmer_bin HMMER_DIR] [--quiet] [--pgap] [--gpipe_org] [--parm PARM] [--threads THREADS] [--debug] [--log LOG]
HELP:    amrfinder --help or amrfinder -h
VERSION: amrfinder --version

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. amr.sh). For example:

#!/bin/bash
set -e
module load amr
export $TMPDIR=/lscratch/$SLURM_JOB_ID
# Protein AMRFinder with no genomic coordinates
amrfinder -p test_prot.fa

# Translated nucleotide AMRFinder (will not use HMMs)
amrfinder -n test_dna.fa

# Protein AMRFinder using GFF to get genomic coordinates and 'plus' genes
amrfinder -p test_prot.fa -g test_prot.gff --plus

# Protein AMRFinder with Escherichia protein point mutations
amrfinder -p test_prot.fa -O Escherichia

# Full AMRFinderPlus search combining results
amrfinder -p test_prot.fa -g test_prot.gff -n test_dna.fa -O Escherichia --plus

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=10G --gres=lscratch:30  amr.sh

Create a swarmfile (e.g. amr.swarm). For example:

amr < amr.in > amr.out
amr < amr.in > amr.out
amr < amr.in > amr.out
amr < amr.in > amr.out

Submit this job using the swarm command.

swarm -f amr.swarm [-g #] [-t #] --module amr