predict.sh

#!/bin/bash
#
#SBATCH --partition=gpu
#
#SBATCH --job-name=dnabertpredict
#SBATCH --output=/home/015861469/dnabert-predict.log
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --mail-type=END

cd examples

export KMER=6
export MODEL_PATH=finetuned-model
export DATA_PATH=sample_data/ft/$KMER-2
export PREDICTION_PATH=/home/015861469/dnabert-predict/output$KMER

python run_finetune.py \
    --model_type dna \
    --tokenizer_name=dna$KMER \
    --model_name_or_path $MODEL_PATH \
    --task_name dna-genome-classification \
    --do_predict \
    --data_dir $DATA_PATH  \
    --max_seq_length 512 \
    --per_gpu_pred_batch_size=128   \
    --output_dir $MODEL_PATH \
    --predict_dir $PREDICTION_PATH \
    --n_process 48