process.exhaustive.kmers.sbatch

#!/bin/bash -l
#SBATCH -J exhaustive
#SBATCH --time 120:00:00
#SBATCH -N 1
#SBATCH --exclude=brncl-[23-31]
#SBATCH --array 0-15
#SBATCH --output %x-%A_%a.out
#SBATCH --error %x-%A_%a.err

mamba activate bowtie2

set -x 
set -e
set -o pipefail


if [[ -z ${FILES} ]]; then
    echo "FILES not set"
    exit 1
fi

if [[ -z ${EX_OUT} ]]; then
    echo "FILES not set"
    exit 1
fi

if [[ -z ${DB_BT2} ]]; then
    echo "DB_BT2 not set"
    exit 1
fi

if [[ ! -f ${FILES} ]]; then
    echo "FILES not found"
    exit 1
fi

mkdir -p ${EX_OUT}

bt2_threads=$((${SLURM_CPUS_PER_TASK} - 2))

python exhaustive.py process-kmers \
    --kmer ${K} \
    --jump ${J} \
    --files ${FILES} \
    --task-id ${SLURM_ARRAY_TASK_ID} \
    --task-count ${SLURM_ARRAY_TASK_COUNT} \
    --threads ${bt2_threads} \
    --db-bt2 ${DB_BT2} \
    --kmers-sam ${EX_OUT}/${SLURM_ARRAY_TASK_ID}.sam


# for f in $(cat ${FILES})
# do
#     zcat ${f}
# done | \
#     python kmer.py ${K} ${J} ${SLURM_ARRAY_TASK_ID} ${SLURM_ARRAY_TASK_COUNT} | \
#     bowtie2 -p ${bt2_threads} \
#         -x ${DB_BT2} \
#         -f - \
#         --seed 42 \
#         --very-sensitive \
#         -k 32 \
#         --np 1 \
#         --mp "1,1" \
#         --rdg "0,1" \
#         --rfg "0,1" \
#         --score-min "L,0,-0.05" \
#         --no-head \
#         --no-unal | \
#             xz -1 -z -c > ${EX_OUT}/${SLURM_ARRAY_TASK_ID}.sam.xz