Frequently Asked Questions

How do I run ARETE in a Slurm HPC environment?

• Set a config file under ~/.nextflow/config to use the slurm executor:

  process {
    executor = 'slurm'
    pollInterval = '60 sec'
    submitRateLimit = '60/1min'
    queueSize = 100
    // If an account is necessary:
    clusterOptions = '--account=<my-account>'
  }

See the Nextflow documentation for a description of these options.

• Now, when running ARETE, you'll need to set additional options if your compute nodes don't have network access - as is common for most Slurm clusters. The example below uses the default test data, i.e. the test profile, for demonstration purposes only.

nextflow run beiko-lab/ARETE \
  --db_cache path/to/db_cache \
  --bakta_db path/to/baktadb \
  -profile test,singularity

Apart from -profile singularity, which just makes ARETE use Singularity/Apptainer containers for running the tools, there are two additional parameters:

• --db_cache should be the location for the pre-downloaded databases used in the DIAMOND alignments (i.e. Bacmet, VFDB, ICEberg2 and CAZy FASTA files) and in the Kraken2 taxonomic read classification.

  • Although these tools run by default, you can change the selection of annotation tools by changing --annotation_tools and skip Kraken2 by adding --skip_kraken. See the parameter documentation for a full list of parameters and their defaults.

• --bakta_db should be the location of the pre-downloaded Bakta database

  • Alternatively, you can use Prokka for annotating your assemblies, since it doesn't require a downloaded database (--use_prokka).

• Do note that there could be memory-related issues when running Nextflow in SLURM environments.

Can I use the ARETE outputs in MicroReact?

Yes you can! In fact, ARETE provides many outputs that can be used in the MicroReact web app. Some of these files are:

• The PopPUNK lineages tree under poppunk_results/poppunk_visualizations/poppunk_visualizations.microreact.

• The reference tree built with FastTree under phylogenomics/reference_tree/core_gene_alignment.tre.

• The annotation feature profile annotation/feature_profile.tsv.gz. This file contains the annotation features in a presence/absence matrix format. Since MicroReact doesn't allow compressed files, just make sure to decompress it before-hand:

gunzip feature_profile.tsv.gz

Make sure to check our output documentation for a full list of outputs and the parameter documentation for a description of parameters to enable and disable these outputs.

Why am I getting this 'docker: Permission denied' error?

Although previous ARETE users have reported this issue, this is neither an issue with Nextflow nor with ARETE itself.

This is most likely due to how Docker permissions are set up on your machine.

• If running on your own machine, take a look at this guide.

• If running on an HPC system, talk to your system administrator or consider running ARETE with Singularity.

My server doesn't have that much memory! How do I change the resource requirements?

Just write a file called nextflow.config in your working directory and add the following to it:

process {
    withLabel:process_low {
        cpus   = 6
        memory = 8.GB
        time   = 4.h
    }
    withLabel:process_medium {
        cpus   = 12
        memory = 36.GB
        time   = 8.h
    }
    withLabel:process_high {
        cpus   = 16
        memory = 72.GB
        time   = 20.h
    }
    withLabel:process_high_memory {
        memory = 200.GB
    }
    withName: MOB_RECON {
        cpus = 2
    }
}

Feel free to change the values above as you wish and then add -c nextflow.config to your nextflow run beiko-lab/ARETE command.

You can point to general process labels, like process_low, or you can point directly to process names, like MOB_RECON. Learn more at our usage documentation or the official nextflow documentation.

How do I add extra parameters when executing a tool in ARETE?

Simple! As above, create a file called nextflow.config in your working directory and add the following to it:

process {
    withName: EVOLCCM {
        ext.args = '--max_abundance 0.8'
    }
}

Then, add -c nextflow.config to your nextflow run beiko-lab/ARETE command. The command above will attach the --max_abundance 0.8 parameter to the execution of the EVOLCCM tool.