Finetuning-ProkBert

Quickstart (HPC)

# 1) Clone
git clone <YOUR_REPO_URL> ldrd-16s-mag-linking
cd ldrd-16s-mag-linking

# 2) Create environment
mamba env create -f envs/ldrd-16s.yml
conda activate ldrd-16s

# 3) Submit SLURM job (single file)
sbatch --export=ALL,REPO_DIR=$PWD,INPUT_FASTA=/path/to/input.fa,OUTPUT_FASTA=$PWD/results/input_no16S.fa,THREADS=8 slurm/remove_16S.sbatch

# (optional) Directory: run as array across all *.fa in data/raw/
N=$(ls -1 data/raw/*.fa 2>/dev/null | wc -l)
sbatch --array=0-$((N-1)) --export=ALL,REPO_DIR=$PWD,IN_DIR=$PWD/data/raw,OUT_DIR=$PWD/results,THREADS=8 slurm/remove_16S_array.sbatch