From f28e6b48b5ae4febe412bbc8b3f80ac9ebea901f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 5 Feb 2019 13:31:45 -0600
Subject: [PATCH] remove tempdir option
---
alignment/markdups.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index e246e60..6338711 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -57,8 +57,8 @@ elif [ $algo == 'fgbio_umi' ]
then
module load fgbio bwa/intel/0.7.15
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
- fgbio -Djava.io.tmpdir=./ GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -e 0 -m 0
- fgbio -Djava.io.tmpdir=./ CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
+ fgbio GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -e 0 -m 0
+ fgbio CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
samtools index ${pair_id}.consensus.bam
samtools fastq -1 ${pair_id}.consensus.R1.fastq -2 ${pair_id}.consensus.R2.fastq ${pair_id}.consensus.bam
gzip ${pair_id}.consensus.R1.fastq
--
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