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quast.sh
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## Summarize assembly with QUAST
out=$1
name=$2
data=$3
pwd=$4
threads=$5
RAM=$6
if [ $RAM -gt 64 ]
then
RAM=64
fi
printf "sh FullPipeline/quast.sh $1 $2 $3 $4 $5 $6\n# "
#############################
mkdir -p ${out}/results/AssemblyQC/Quast
### NOTE THAT QUAST ONLY ALLOWS 64 CORES MAX
if [[ $threads -gt 64 ]]
then
threads=64
fi
echo """
#!/bin/sh
## name of Job
#PBS -N QUAST_${name}
## Redirect output stream to this file.
#PBS -o ${out}/log/Quast_${name}_log.txt
## Stream Standard Output AND Standard Error to outputfile (see above)
#PBS -j oe
## Select ${threads} cores and ${RAM}gb of RAM
#PBS -l select=1:ncpus=${threads}:mem=${RAM}g
######## load dependencies #######
module load Assembly/Quast-5.1.0rc1
######## run analyses #######
## Go to pwd
cd ${pwd}
quast.py \
--output-dir ${out}/results/AssemblyQC/Quast \
--threads ${threads} \
--eukaryote \
-f \
${out}/output/${name}_${data}.fa
""" > ${out}/shell/qsub_quast_${name}.sh
qsub ${out}/shell/qsub_quast_${name}.sh