README-debug-megalodon.md

gcloud compute instances create megalodon \
    --machine-type a2-highgpu-2g \
    --zone us-central1-a \
    --boot-disk-size 2000GB \
    --image-family cos-97-lts \
    --image-project cos-cloud \
    --maintenance-policy TERMINATE --restart-on-failure 
    
    gcloud compute ssh --zone us-central1-a megalodon
    
    # Localize inputs
    # Reads
    toolbox gsutil cp gs://aryeelab-nanopore/large-test/HEPG2-H3K27me3test.tar.gz /media/root/home/$USER/
    # Genome FASTA
    toolbox gsutil cp gs://aryeelab-nanopore/griffinlab/references/GCA_000001405.15_GRCh38_full_analysis_set.fna /media/root/home/$USER/
    # Models
    toolbox gsutil cp gs://aryeelab-nanopore/griffinlab/references/basecall.tar.gz /media/root/home/$USER/
    
    # Install GPU drivers
    sudo cos-extensions install gpu
    sudo mount --bind /var/lib/nvidia /var/lib/nvidia
    sudo mount -o remount,exec /var/lib/nvidia

    # Configure artifact registry credentials
    docker-credential-gcr configure-docker --registries us-central1-docker.pkg.dev

    docker run --rm -it \
      --volume /home/$USER:/work \
      --volume /var/lib/nvidia/lib64:/usr/local/nvidia/lib64 \
      --volume /var/lib/nvidia/bin:/usr/local/nvidia/bin \
      --device /dev/nvidia0:/dev/nvidia0 \
      --device /dev/nvidia-uvm:/dev/nvidia-uvm \
      --device /dev/nvidiactl:/dev/nvidiactl \
      us-central1-docker.pkg.dev/aryeelab/docker/megalodon
      
	# In container
    cd /work  
      
    reads="HEPG2-H3K27me3test.tar.gz"
    model="basecall.tar.gz"
    genome="GCA_000001405.15_GRCh38_full_analysis_set.fna.gz"
    modmotifs="--mod-motif Z CG 0 --mod-motif Y A 0"
    device="cuda:all --processes 10"

    nvidia-smi
    mkdir ./in
    tar zxvf ${reads} -C ./in
    mkdir ./out
    mkdir ./basecall_models
    tar zxvf ${model} -C ./basecall_models
    time megalodon \
    ./in \
    --output-directory "./out" \
    --overwrite \
    --guppy-server-path /usr/bin/guppy_basecall_server \
    --guppy-params "-d ./basecall_models" \
    --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg \
    --outputs basecalls mappings mod_mappings mods per_read_mods \
    --reference ${genome} ${modmotifs} \
    --devices ${device}