#!/bin/bash
#
#SBATCH --nodes=1
#SBATCH --time=2-0
#SBATCH --ntasks=32 # Number of cores
#SBATCH --mem=120000 # Memory pool for all cores (see also --mem-per-cpu)
#SBATCH --partition=production # Partition to submit to
#SBATCH --reservation=genome_workshop
#SBATCH --account=genome_workshop
#SBATCH --output=slurmout/rc-%N-%j.out # File to which STDOUT will be written
#SBATCH --error=slurmout/rc-%N-%j.err # File to which STDERR will be written

hostname

start=`date +%s`

echo "My SLURM_JOB_ID: $SLURM_JOB_ID"


THREADS=${SLURM_NTASKS}


aklog
module load racon/1.4.3
module load minimap2/2.17
module load samtools/1.9
hostname

export baseP=/share/workshop/genome_assembly/${USER}/Nanopore
export seqP=$baseP/02-QC
export outP=$baseP/04-RACON

if [ ! -d "$outP" ]
then
  mkdir -p $outP
fi

finished=$1

if [ $finished == "NO" ]
then
  export asmP=$baseP/03-SHASTA/run1-Linked
  mkdir -p $asmP
  ln -s /share/workshop/genome_assembly/jli/Nanopore/03-SHASTA/run1/* /share/workshop/genome_assembly/${USER}/Nanopore/03-SHASTA/run1-Linked/.
else
  export asmP=$baseP/03-SHASTA/run1
fi


## align
minimap2 -t ${THREADS} -a $asmP/Assembly.fasta $seqP/*.fastq |samtools sort -@ ${THREADS} -m 10G -O SAM -o $outP/minialign.sorted.sam -
cat $seqP/*.fastq > $outP/input.fq

cd $outP
racon -m 8 -x -6 -g -8 -w 500 -t ${THREADS} -u ./input.fq ./minialign.sorted.sam $asmP/Assembly.fasta > racon.polished.fa



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