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#!/bin/sh -l
# Submit to the rascals queue
#$ -q *@@rascals.h
# Name of the job
#$ -N bz2compact
# Execute the script from the current directory
#$ -cwd
# Combine SGE error and output files.
#$ -j y
# Memory resource requirements (2Gb more than what Java heap is set to below is strongly advised)
#$ -l h_vmem=3g
# Number of threads/cpus
#$ -pe smp 2
cd $TMP
bzcat -f ${DATA_DIR}/${BASENAME}.fastq.bz2 >${BASENAME}.fastq
$GOBY 1g fasta-to-compact --quality-encoding ${QUALITY_ENCODING} ${BASENAME}.fastq
cp ${BASENAME}.compact-reads ${DATA_DIR}/
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