Fantasia

Functional ANnoTAtion based on embedding space SImilArity

FANTASIA is an advanced pipeline designed for automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and similarity searches in vector databases to associate Gene Ontology (GO) terms with proteins.

FANTASIA v4

Script

The following script is an adaptation for IFB of the one called cesga_array.sh provided by Francisco Miguel Perez Canales:

📝 ifb_array.sh

#!/bin/bash
#SBATCH -p gpu
#SBATCH -c 32
#SBATCH --gres={{ gpu_profile_ex }}:1
#SBATCH --mem=64G
#SBATCH -t 12:00:00
#SBATCH --job-name=fantasia_job
#SBATCH --output=fantasia_%j.out
#SBATCH --error=fantasia_%j.err

################################################################################
# FANTASIA job script for CESGA (SLURM GPU partition)
#
# This script launches the full FANTASIA functional annotation pipeline using:
#
# - PostgreSQL with pgvector (run via Apptainer container)
# - RabbitMQ (run via Apptainer container)
# - FANTASIA (run via Apptainer container with GPU support)
#
# All services are isolated and launched locally within the job node,
# using bind mounts to persistent storage on LUSTRE.
#
# NOTE: This script is intended to be submitted via `sbatch` on CESGA's SLURM system.
################################################################################
# =======================

# Load input parameters

# =======================

PARAM_FILE="./experiments.tsv"
IFS=$'\t' read -r INPUT OUTPUT EXTRA <<< "$(sed -n "${SLURM_ARRAY_TASK_ID}p" "$PARAM_FILE")"

if [ -z "$INPUT" ] || [ -z "$OUTPUT" ]; then
echo "❌ ERROR: Entrada no válida en línea $SLURM_ARRAY_TASK_ID del fichero de parámetros"
exit 1
fi

echo "📥 Input file: $INPUT"
echo "📤 Output name: $OUTPUT"
echo "⚙️  Extra params: $EXTRA"

STORE=$PWD

# =======================
# Define working directories
# =======================
PROJECT_DIR="$STORE/FANTASIA"
EXECUTION_DIR="$STORE/fantasia"
SHARED_MEM_DIR="/tmp/fantasia"
POSTGRESQL_DATA="$SHARED_MEM_DIR/data"
POSTGRESQL_SOCKET="$SHARED_MEM_DIR/socket"
RABBITMQ_DATA_DIR="$STORE/fantasia_rabbitmq"
CONFIG_FILE="$PROJECT_DIR/fantasia/config.yaml"

# Apptainer container images
PGVECTOR_IMAGE="$PROJECT_DIR/pgvector.sif"
RABBITMQ_IMAGE="$PROJECT_DIR/rabbitmq.sif"
FANTASIA_IMAGE="$PROJECT_DIR/fantasia.sif"

DB_NAME="BioData"
PG_PORT=5432

# =======================
# Environment sanity check
# =======================
echo "📂 Current working directory:"
pwd
ls -l

# Clone FANTASIA repo if missing
if [ ! -d "$PROJECT_DIR" ]; then
    echo "🚀 Cloning FANTASIA from GitHub..."
    git clone https://github.com/CBBIO/FANTASIA.git "$PROJECT_DIR"
fi

cd "$PROJECT_DIR" || exit 1

# =======================
# Build containers if not present
# =======================
if [ ! -f "$PGVECTOR_IMAGE" ]; then
    echo "🔨 Building pgvector container..."
    apptainer build "$PGVECTOR_IMAGE" docker://pgvector/pgvector:pg16
fi

if [ ! -f "$RABBITMQ_IMAGE" ]; then
    echo "🔨 Building RabbitMQ container..."
    apptainer build "$RABBITMQ_IMAGE" docker://rabbitmq:management
fi

if [ ! -f "$FANTASIA_IMAGE" ]; then
    echo "🔨 Building FANTASIA container..."
    apptainer build --disable-cache "$FANTASIA_IMAGE" docker://frapercan/fantasia:latest
fi

# =======================
# Launch PostgreSQL (pgvector)
# =======================
echo "🚀 Starting PostgreSQL (pgvector)..."

PGDATA_HOST="$STORE/pgdata_pgvector"
PG_RUN="$STORE/pg_run"

rm -rf "$PGDATA_HOST"
mkdir -p "$PGDATA_HOST" "$PG_RUN"

nohup apptainer run \
  --env POSTGRES_USER=usuario \
  --env POSTGRES_PASSWORD=clave \
  --env POSTGRES_DB="$DB_NAME" \
  --bind "$PGDATA_HOST:/var/lib/postgresql/data" \
  --bind "$PG_RUN:/var/run/postgresql" \
  "$PGVECTOR_IMAGE" > postgres.log 2>&1 &

# =======================
# Launch RabbitMQ
# =======================
echo "🚀 Starting RabbitMQ..."

rm -rf "$RABBITMQ_DATA_DIR"
mkdir -p "$RABBITMQ_DATA_DIR"

nohup apptainer run \
  --bind "$RABBITMQ_DATA_DIR:/var/lib/rabbitmq" \
  "$RABBITMQ_IMAGE" > rabbitmq.log 2>&1 &

# =======================
# Wait for services to become available
# =======================
echo "⏳ Waiting for services to initialize..."
sleep 30

# =======================
# Run FANTASIA pipeline
# =======================
mkdir -p "$EXECUTION_DIR"

if [ ! -f "$CONFIG_FILE" ]; then
    echo "❌ ERROR: Configuration file not found at $CONFIG_FILE"
    exit 1
fi

echo "✅ Found configuration file: $CONFIG_FILE"
echo "📂 Listing FANTASIA contents:"
ls -l "$PROJECT_DIR/fantasia/"

apptainer exec --nv --bind "$EXECUTION_DIR:/fantasia" "$FANTASIA_IMAGE" \
    fantasia initialize

apptainer exec --nv --bind "$EXECUTION_DIR:/fantasia" "$FANTASIA_IMAGE" \
    fantasia run --input "$INPUT" --prefix "$OUTPUT" $EXTRA

# =======================
# Cleanup services on exit
# =======================
cleanup() {
    echo "🧹 Cleaning up background services..."

    if pgrep -f "$POSTGRESQL_DATA" > /dev/null; then
        echo "🛑 Stopping PostgreSQL..."
        pkill -f "$POSTGRESQL_DATA"
    fi

    if pgrep -f "rabbitmq-server" > /dev/null; then
        echo "🛑 Stopping RabbitMQ..."
        pkill -f "rabbitmq-server"
    fi

    if [[ -d "$SHARED_MEM_DIR" ]]; then
        echo "🗑️ Removing shared memory directory: $SHARED_MEM_DIR"
        rm -rf "$SHARED_MEM_DIR"
    fi
}

Full example of usage

Prerequisites

You will need a SLURM account with an access to the GPU SLURM partition.

Inputs

sample.fasta from github.com/CBBIO/FANTASIA

>DFRU1_DN0_c0_g1_i4.p1
MSGVPVPVPTLVDQKIAGKKVVVFSKTSCGYCTKVKNVLKQYILKPDDYEVVEMDTDYSSDMSAMQDYLQELTGARSVPR
VFVNGKSIGGHDDTVARHKAGKLGLEKKI
>Q9CQV8 10090
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLILNATQAESKVFY
LKMKGDYFRYLSEVASGENKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
AGEGEN
>P62259 10090
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW
RIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVF
YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF
YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE
EQNKEALQDVEDENQ

📝 experiments.tsv

/shared/projects/admin/2025-10_test_fantasia/sbatch_strategy/sample.fasta   sample

Run

sbatch ifb_array.sh

🚀