v1 Installing AMRFinder

Installation Summary

AMRFinder requires HMMER, BLAST+, Linux, and perl. We provide Linux binaries, and the source code is available if you want to compile it yourself, though we haven't extensively tested compiling AMRFinder on other systems and aren't supporting non-Linux systems at this time.

New! Install AMRFinder via Bioconda

Prerequisites

We recommend using Bioconda to install the prerequisites and provide instructions for how to do that below. The executables for BLAST, HMMER, and Perl will need to be in your path. See the Troubleshooting section below to test them. Note, it's not a prerequisite, but these instructions use Borne shell style syntax (e.g., that from bash). If you're using another shell syntax you might have to modify them slightly.

Bioconda

While not strictly a prerequisite Bioconda is how we recommend installing the prerequisites. If you don''t have bioconda already installed you should run the following

~$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
~$ bash ./Miniconda3-latest-Linux-x86_64.sh # Follow prompts to accept license, choose install path, and allow the new bin directory to be added to .bashrc
~$ export PATH=$HOME/miniconda3/bin:$PATH # Change to match installation location, if not default.
~$ conda config --add channels defaults
~$ conda config --add channels bioconda
~$ conda config --add channels conda-forge

Install the prerequisites

With bioconda the three prerequisites can be installed in one command

~$ conda install -y blast hmmer perl

Installing AMRFinder

~$ mkdir amrfinder && cd amrfinder
~/amrfinder$ curl -sL https://github.com/ncbi/amr/releases/download/amrfinder_v1.04/amrfinder_binaries_v1.04.tar.gz | tar xvz
~/amrfinder$ ./amrfinder.pl -U
~/amrfinder$ ./amrfinder.pl -p test_prot.fa

Testing your installation

~/amrfinder$ ./amrfinder.pl -p test_prot.fa

You should see something like test_prot.expected

Target identifier	Gene symbol	Protein name	Method	Target length	Reference protein length	% Coverage of reference protein	% Identity to reference protein	Alignment length	Accession of closest protein	Name of closest protein	HMM id	HMM description
blaOXA-436_partial	blaOXA	OXA-48 family class D beta-lactamase	PARTIAL	233	265	87.92	100.00	233	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NF000387.2	OXA-48 family class D beta-lactamase
blaPDC-114_blast	blaPDC	PDC family class C beta-lactamase	BLAST	397	397	100.00	99.75	397	WP_061189306.1	class C beta-lactamase PDC-114	NF000422.2	PDC family class C beta-lactamase
blaTEM-156	blaTEM-156	class A beta-lactamase TEM-156	ALLELE	286	286	100.00	100.00	286	WP_061158039.1	class A beta-lactamase TEM-156	NF000531.2	TEM family class A beta-lactamase
nimIJ_hmm	nimIJ	NimIJ family nitroimidazole resistance protein	HMM	166	NA	NA	NA	NA	NA	NA	NF000262.1	NimIJ family nitroimidazole resistance protein
vanG	vanG	D-alanine--D-serine ligase VanG	EXACT	349	349	100.00	100.00	349	WP_063856695.1	D-alanine--D-serine ligase VanG	NF000091.3	D-alanine--D-serine ligase VanG

~/amrfinder$ ./amrfinder -n test_dna.fa

You should see something like test_dna.expected

Target identifier	Contig id	Start	Stop	Strand	Gene symbol	Protein name	Method	Target length	Reference protein length	% Coverage of reference protein	% Identity to reference protein	Alignment length	Accession of closest protein	Name of closest protein	HMM id	HMM description
contig1	contig1	101	958	+	blaTEM-156	class A beta-lactamase TEM-156	ALLELE	286	286	100.00	100.00	286	WP_061158039.1	class A beta-lactamase TEM-156	NF000531.2	TEM family class A beta-lactamase
contig2	contig2	1	1191	+	blaPDC	PDC family class C beta-lactamase	BLAST	397	397	100.00	99.75	397	WP_061189306.1	class C beta-lactamase PDC-114	NF000422.2	PDC family class C beta-lactamase
contig3	contig3	101	802	+	blaOXA	OXA-48 family class D beta-lactamase	PARTIAL	234	265	88.30	100.00	234	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NF000387.2	OXA-48 family class D beta-lactamase
contig4	contig4	101	1147	+	vanG	D-alanine--D-serine ligase VanG	EXACT	349	349	100.00	100.00	349	WP_063856695.1	D-alanine--D-serine ligase VanG	NF000091.3	D-alanine--D-serine ligase VanG

Troubleshooting

To run AMRFinder all of the prerequisites must be installed and in your PATH. We also recommend placing the AMRFinder executables in your path (e.g., export PATH=~/amrfinder)