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EBI-Metagenomics / genomes-catalogue-pipeline

MGnify genome analysis pipeline
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No valid AMRFinder database is found #69

Closed akques closed 9 months ago

akques commented 9 months ago

Hi, I had one question about the installation of this pipeline

I feel quite confused because, during the actual installation process, the README did not mention the need to install AMRFinder database. However, in the nextflow.config file, it requires me to specify the path to this database. Following your earlier suggestion, I downloaded the corresponding version of the database from the amrfinder official websiteand put it under this diractory: /media/chenwen/miniconda3/share/amrfinderplus/data/2023-02-23.1Yet, during the test of this pipleine , I encountered issues. 

  *** ERROR ***
  No valid AMRFinder database is found.
  This directory (or symbolic link to directory) is not found: /media/chenwen/miniconda3/share/amrfinderplus/data/2023-02-23.1
  To download the latest version to the default directory run: amrfinder -u

  HOSTNAME: 410be4c3662f
  SHELL: ?
  PWD: /mnt/chenwen/02.program/10.mgnify_test/00.script/work/f3/f342e386c93a2c661490879fd67962
  PATH: /usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin
  Progam name:  amrfinder
  Command line: amrfinder --plus -n MGYG000000000.fna -p MGYG000000000.faa -g MGYG000000000.gff -d /media/chenwen/miniconda3/share/amrfinderplus/data/2023-02-23.1 -a prokka --output MGYG000000000_amrfinde
rplus.tsv --threads 1

Work dir:
  /mnt/chenwen/02.program/10.mgnify_test/00.script/work/f3/f342e386c93a2c661490879fd67962

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Upon inspecting the modules/amrfinder_plus.nf file, I noticed the use of the amrfinder image. Hence, I suspect that my local database path might not be properly mapped into this image. However, I am uncertain if this is the issue and do not know how to resolve it.

Thank you very much in advance. Best regards, May

mberacochea commented 9 months ago

Hi @akques,

The reference databases are specified in the pipeline nextflow.config file. We have defined an EBI nextflow configuration profile, which is the one used in our HPC cluster.

For AMRFinder Plus, the database you should download is: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/3.11/2023-02-23.1/ (I'll include it in the README file). The path to the downloaded files needs to be specified in the param amrfinder_plus_db.

Cheers,