#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=24
#SBATCH --time=5-12
#SBATCH --mem=80000 # Memory pool for all cores (see also --mem-per-cpu)
#SBATCH --partition=production
#SBATCH --reservation=meta_workshop
#SBATCH --account=workshop
#SBATCH --output=slurmout/mtb_%A_%a.out # File to which STDOUT will be written
#SBATCH --error=slurmout/mtb_%A_%a.err # File to which STDERR will be written


start=`date +%s`
hostname

export baseP=/share/workshop/meta_workshop/$USER/meta_example
export seqP=$baseP/02-DNA-rmhost
export asmP=$baseP/03-Megahit-DNA
export outP=$baseP/04-MetaBat

SAMPLE=`head -n ${SLURM_ARRAY_TASK_ID} samples.txt | tail -1 `

echo $SAMPLE

if [ ! -e $outP/${SAMPLE} ]; then
    mkdir -p $outP/${SAMPLE}
fi


module load metabat/2.12.1
module load bowtie2/2.4.2
module load samtools/1.11

call="bowtie2-build --threads ${SLURM_CPUS_PER_TASK} $asmP/${SAMPLE}/${SAMPLE}.contigs.fa $asmP/${SAMPLE}/${SAMPLE}.contigs"

echo $call
eval $call

nbt=$(( ${SLURM_CPUS_PER_TASK} - 6 ))

call="bowtie2 -x $asmP/${SAMPLE}/${SAMPLE}.contigs \
      -1 $seqP/${SAMPLE}/${SAMPLE}_R1.fastq -2 $seqP/${SAMPLE}/${SAMPLE}_R2.fastq \
      --end-to-end -p ${nbt} |samtools view -bh - |samtools sort -@ 4 -m2G -o $outP/${SAMPLE}/${SAMPLE}.bam - "

echo $call
eval $call

call="jgi_summarize_bam_contig_depths --outputDepth $outP/${SAMPLE}/depth.txt $outP/${SAMPLE}/${SAMPLE}.bam"

echo $call
eval $call


call="metabat2 -i $asmP/${SAMPLE}/${SAMPLE}.contigs.fa -a $outP/${SAMPLE}/depth.txt -o $outP/${SAMPLE}/bin -v"


echo $call
eval $call

end=`date +%s`
runtime=$((end-start))
echo Runtime: $runtime seconds