srun-metaspades.sh

srun-metaspades.sh

#!/bin/bash
NODE=bio
THREADS=7 #7 for bio, 24 for t1small
MEM=200 #128 max for t1small, 200+ for bio

mkdir -p spades-assembly
DIR='.'

#NPRB_meta_TBS.04.MEIO.R1.trimmed.fastq.gz
for PREFIX in `ls *.trimmed.fastq.gz | cut -f1-3 -d'.' | sort -u `; do

    F1=($PREFIX"."*R1.trimmed*)
    R1=($PREFIX"."*R2.trimmed*)

    #echo "${F1[*]}"
    #echo "${R1[*]}"

#    FINDIR=`dirname $F1`"_"`basename $F1 | cut -f2 -d'_'`
    OUTDIR=$PREFIX"_"`date +'%F-%H-%M-%S'`
    if [ -e spades-assembly/metaspades_$FINDIR*/scaffolds.fasta ]; then continue; fi

    SPADESCMD="~/apps/SPAdes-3.11.0-Linux/bin/metaspades.py -o spades-assembly/metaspades_$OUTDIR -t $THREADS -m $MEM --tmp-dir /tmp -k21,33,55,67,77,89,99,121 "

    J=$((${#F1[@]}-1))
    for I in `seq 0 $J`; do
        SPADESCMD=$SPADESCMD" --pe1-1 ${F1[$I]} --pe1-2 ${R1[$I]} "
        echo -e $SPADESCMD

        sbatch --partition=$NODE --ntasks=$THREADS --tasks-per-node=$THREADS --mem=$MEMG <<-EOF
#!/bin/sh
eval "$SPADESCMD"
EOF

    done
done
done

#mkdir -p corrected/$DIR
#mv spades-assembly/metaspades_$OUTDIR/corrected/*.gz corrected/$DIR/
#rm -rf spades-assembly/metaspades_$OUTDIR/K*