-
Notifications
You must be signed in to change notification settings - Fork 0
/
s4_markdup.sl
52 lines (41 loc) · 1.58 KB
/
s4_markdup.sl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
#!/bin/bash
#SBATCH -J s4_MarkDup
#SBATCH -A nesi00319 # Project Account
#SBATCH --time=05:59:00 # Walltime
#SBATCH --mem-per-cpu=24003 # memory/cpu (in MB)
#SBATCH --cpus-per-task=1 # 12 OpenMP Threads
#SBATCH --nodes=1
#SBATCH -C sb
#SBATCH --mail-user=murray.cadzow@otago.ac.nz
#SBATCH --mail-type=FAIL,TIME_LIMIT_90
# Murray Cadzow
# University of Otago
# 20 Oct 2015
# Matt Bixley
# University of Otago
# Jun 2016
echo markdup start $(date "+%H:%M:%S %d-%m-%Y")
DIR=$1
sample=$2
chr=$(cat ~/NeSI_GATK/contigs_h37.txt | awk -v line=${SLURM_ARRAY_TASK_ID} '{if(NR == line){print}}')
export OPENBLAS_MAIN_FREE=1
source ~/NeSI_GATK/gatk_references.sh
module load SAMtools/1.2-goolf-1.5.14
module load picard/2.1.0
if ! srun samtools view -bh $DIR/temp/${sample}_gathered.bam $chr > $DIR/temp/$chr.bam ; then
echo "contig bam creation failed"
echo "contig bam creation failed" >> $DIR/final/failed.txt
exit 1
fi
if ! srun java -Xmx19g -jar $EBROOTPICARD/picard.jar MarkDuplicates \
INPUT=$DIR/temp/${chr}.bam \
OUTPUT=$DIR/temp/${sample}_dedup_reads_${chr}.bam \
METRICS_FILE=$DIR/logs/metrics.txt \
CREATE_INDEX=true \
TMP_DIR=$DIR ; then
echo "markdup failed"
echo "markdup failed" >> $DIR/final/failed.txt
exit 1
fi
rm $DIR/temp/${chr}.bam
echo markdup finish $(date "+%H:%M:%S %d-%m-%Y")