From 79dc4690d466e0caf234644a49d9ebf8380be855 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sun, 5 Aug 2018 14:00:13 -0500
Subject: [PATCH] multithreaded bamqc
---
alignment/bamqc.sh | 8 ++++----
alignment/starfusion.sh | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 86d1643..82346c7 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -44,15 +44,15 @@ fi
if [[ $nuctype == 'dna' ]]; then
module load bedtools/2.26.0 picard/2.10.3
- samtools view -b --threads $SLURM_CPUS_ON_NODE -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
- samtools index ${pair_id}.ontarget.bam
+ samtools view -@ $SLURM_CPUS_ON_NODE -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
+ samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.ontarget.bam
#samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
java -Xmx64g -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${sbam} HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${index_path}/genome.fa OUTPUT=${pair_id}.hist.txt
java -Xmx64g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
java -Xmx64g -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt
- samtools view -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
+ samtools view -@ $SLURM_CPUS_ON_NODE -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
bedtools coverage -sorted -g ${index_path}/genomefile.txt -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt
grep ^all ${pair_id}.covhist.txt > ${pair_id}.genomecov.txt
- samtools view ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
+ samtools view -@ $SLURM_CPUS_ON_NODE ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
fi
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 070e8d3..86fc7ea 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -33,7 +33,7 @@ fi
index_path=${refgeno}/CTAT_lib/
baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
-module add python/2.7.x-anaconda star/2.5.2b
+module add python/2.7.x-anaconda star/2.5.2b bedtools/2.26.0
STAR-Fusion --genome_lib_dir ${index_path} --left_fq ${fq1} --right_fq ${fq2} --output_dir star_fusion &> star_fusion.err
mv star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
--
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