Test your installation

Make sure amrfinder and the dependencies blast and HMMER are executable and in your path. If you installed via bioconda you may need to run:

source ~/miniconda3/bin/activate amrfinder

Make sure you have the latest AMRFinder database files:

amrfinder -u

The bioconda installation doesn't yet include the test files, so if you need to you can use the following commands to download them:

    BASE_URL=https://raw.githubusercontent.com/ncbi/amr/master
    curl --silent -L \
       -O ${BASE_URL}/test_dna.fa \
       -O ${BASE_URL}/test_prot.fa \
       -O ${BASE_URL}/test_prot.gff \
       -O ${BASE_URL}/test_both.expected \
       -O ${BASE_URL}/test_dna.expected \
       -O ${BASE_URL}/test_dna_mut_all.expected \
       -O ${BASE_URL}/test_prot.expected \
       -O ${BASE_URL}/test_amrfinder.sh

Then to test the version of amrfinder that is in your PATH (e.g., installed with Bioconda) type

bash test_amrfinder.sh path

Or if you're in the source or binary directory you downloaded from github and want to test ./amrfinder use:

bash test_amrfinder.sh

If the tests all pass the output will end with

Success!

Troubleshooting

Make sure the dependencies are executable

The most common issues are that the AMRFinderPlus can't find blast or HMMER binaries. Make sure you can run the following:

blastp -help

If that does not print out a long help message from blastp then AMRFinder may not know where to find your blast executables. If you installed blast via bioconda then running source ~/miniconda3/bin/activate may fix this issue.

hmmsearch -h

If that command doesn't print a help message from HMMER then AMRFinder may not know where to find the HMMER executables. If you installed HMMER via bioconda then running source ~/miniconda3/bin/activate may fix this issue.

Download the latest database

amrfinder -u

Try updating to the latest version

conda update -c bioconda -y ncbi-amrfinderplus

Email

If you are still having trouble installing AMRFinderPlus or have any questions let us know by emailing us at [email protected].