Samtools

#!/bin/bash -x

#PBS -N samtools
#PBS -q batch
#PBS -l walltime=72:00:00
#PBS -l feature=fastest_nodes
#PBS -j oe
####PBS -A samtools
#PBS -o job

### Switch to the working directory; by default TORQUE launches processes from your home directory.
cd $PBS_O_WORKDIR
# echo Working directory is $PBS_O_WORKDIR

# Calculate the number of processors allocated to this run.
NPROCS=`wc -l < $PBS_NODEFILE`
#### PBS_NUM_PPN        Number of procs per node allocated to the job
module load samtools-1.9

export reference=/mnt/home/usr/references/refseq.fasta
export INPATH=/mnt/usr/infiles
export INPATH1=/mnt/usr/dir1
mkdir -p $INPATH1
export INPATH2=/mnt/usr/dir2
mkdir -p $INPATH2
export INPATH3/mnt/usr/dir3
mkdir -p $INPATH3
export INPATH4=/mnt/usr/dir3
mkdir -p $INPATH4
export INPATH5=/mnt/usr/dir4
mkdir -p $INPATH5
export BAM=/mnt/usr/dir6_pathtoBAM
mkdir -p $BAM
export INPATH7=/mnt/usr/dir7
mkdir -p $INPATH7
export INPATH8=/mnt/usr/dir8
mkdir -p $INPATH8
export INPATH9=/mnt/usr/dir9
mkdir -p $INPATH9

shopt -s nullglob
for dir in $INPATH{/,/*} ;
do
for file in $dir/*.sam ;
do

        echo inpath $INPATH
        bname=$(basename $file ".sam")
        dirname=$(basename $dir)
        echo dirname: $dir
        echo bname: $bname
        outpath=$BAM/$dirname
        echo outpath: $outpath
        mkdir -p $outpath
        chmod u+rwx $outpath
        echo dir: $dir
        echo inpath $INPATH
        bname=$(basename $file ".sam")
        echo $bname
        bamfile=$INPATH1/$bname"bam1.bam"
        namesort=$INPATH2/$bname"_sorted.bam"
        fixmate=$INPATH4/$bname"_sorted_fixmate.bam"
        positionsort=$INPATH5/$bname"_sorted_fixmate_position.bam"
        markdup=$outpath/$bname".bam"
        stats=$INPATH8/$bname".txt"

        echo $file
        samtools view -bT $reference $file > $bamfile
        echo $bamfile
        samtools sort -n -@ ${PBS_NUM_PPN} $bamfile > $namesort
        echo $namesort
        samtools fixmate -m -@ ${PBS_NUM_PPN} $namesort $fixmate
        echo $fixmate
        samtools sort -@ ${PBS_NUM_PPN} $fixmate > $positionsort
        echo $positionsort
        samtools markdup -@ ${PBS_NUM_PPN} $positionsort $markdup
        echo $markdup
        samtools index -@ ${PBS_NUM_PPN} $markdup
        echo $markdup
        samtools flagstat $markdup > $stats
        echo $stats
done
done