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Taxon binning benchmarking

Modules

  • Autometa v1.0.3
  • Autometa v2.0.2
  • mmseqs2
  • kraken2
  • diamond

Benchmark

First locate taxon binning directory

# For example...
cd ${HOME}/metaBenchmarks/taxon-binning

Run nextflow benchmarking for taxon-binning with taxon-binning-benchmarks env (conda activate taxon-binning-benchmarks).

See Setup for details on configuring the taxon-binning-benchmarks compute environment

nextflow run main.nf -c simulated.config -profile slurm -resume

Setup

  1. create env
  2. activate env
  3. build autometa v1.0.3 docker image

Create env

conda env create -f=environment.yml

Activate env

conda activate taxon-binning-benchmarks

Create env for Autometa v1.0.3

1. Build docker image

docker build \
    https://github.com/KwanLab/Autometa.git#c85ab9673345f62e9d6a7e1aecb2d1c4e1b0c598#c85ab9673345f62e9d6a7e1aecb2d1c4e1b0c598 \
    -t jasonkwan/autometa:1.0.3

Now setup autometa_v1 env specifically for nextflow execution

2. Install procps in built docker image

# 1. Run a container
docker run --rm -it jasonkwan/autometa:1.0.3
# 2. Install procps in container
apt-get update && apt install -y procps && apt-get clean
# Keep container running...

3. Commit container as new image

(Open a new terminal to tag the running container)

# 3. Check that container is still running and get container ID
docker ps -a
# 4. Commit container to image name with procps installed
# My container ID ended up being 24c4931c82a5
docker commit -m "Add procps for nextflow execution" 24c4931c82a5 jasonkwan/autometa:1.0.3

AMBER docker image creation

docker build taxon_binning/docker/amber -f taxon_binning/docker/amber/Dockerfile -t cami-challenge/amber

Running AMBER on Autometa taxon_binning CAMI2 results

cami_samples=(marmgCAMI2_short_read_pooled_gold_standard_assembly \
    marmgCAMI2_short_read_pooled_megahit_assembly \
    strmgCAMI2_short_read_pooled_gold_standard_assembly \
    strmgCAMI2_short_read_pooled_megahit_assembly)

for sample in ${cami_samples};do
    if [[ $sample == *"strmg"* ]]; then
        ground_truths="${HOME}/metaBenchmarks/data/cami/strain_madness/ground_truth"
        assembly="gsa_pooled_mapping.binning"
        # if [[ $sample == *"gold_standard"* ]]; then
        #     assembly="gsa_pooled_mapping.binning"
        # else
        #     assembly="strain_madness_megahit.binning"
        # fi
    else
        ground_truths="${HOME}/metaBenchmarks/data/cami/marine/ground_truth"
        assembly="gsa_pooled_mapping_short.binning"
        # if [[ $sample == *"gold_standard"* ]]; then
        #     assembly="gsa_pooled_mapping_short.binning"
        # else
        #     assembly="marine_megahit.binning"
        # fi
    fi
    results="${HOME}/metaBenchmarks/taxon-binning/nf-taxon-binning-benchmarks/${sample}"
    ncbiDir="${HOME}/metaBenchmarks/data/cami/databases"
    docker run --rm \
        -v $results:/results:rw \
        -v $ground_truths:/ground_truths:ro \
        -v $ncbiDir:/ncbi:rw \
        --user=$(id -u):$(id -g) \
        cami-challenge/amber \
        --gold_standard_file ground_truths/$assembly \
        --output_dir /results/amber-output \
        --ncbi_dir /ncbi \
        /results/${sample}.autometa_v2.taxonomy.binning
done

OPAL docker image creation

docker build taxon-binning/docker/opal -f taxon-binning/docker/opal/Dockerfile -t cami-challenge/opal