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|
#!/bin/bash
USAGE="$0 /path/to/metabat2 [ binPrefix ]"
mb2=$(realpath $1)
if [ ! -x "$mb2" ]
then
echo "$USAGE" 1>&2
echo "Could not execute '$mb2'" 1>&2
exit 1
fi
git=$(which git 2>/dev/null || true)
gitver=
if [ -x "$git" ]
then
gitver=$(${git} describe --tags --dirty 2>/dev/null || true)
[ -z "$gitver" ] || gitver="-$gitver"
fi
binPrefix=$2
[ -n "$binPrefix" ] || binPrefix=standard$gitver
invokedas="'$0 $@'"
# Resolve the base path and bootstrap the environment
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
echo "Starting $invokedas at $(date)"
set -e
set -o pipefail
onerr()
{
echo "uh oh something went wrong with '$invokedas' at $(date)" 1>&2
trap "" 0
exit 1
}
trap onerr 0 1 2 3 15
if [ -n "$SCRATCH" ] && [ -w "$SCRATCH" ]
then
WORKDIR=/$SCRATCH/$USER-metabat-standards
else
WORKDIR=/tmp/$USER-metabat-standards
fi
mkdir -p $WORKDIR
cd $WORKDIR
echo "Saving files to $(pwd) and using binPrefix=$binPrefix"
for case in CASE1 CASE2 CASE3
do
if [ ! -d $case ]
then
mkdir $case.tmp
cd $case.tmp
wget https://portal.nersc.gov/dna/RD/Metagenome_RD/MetaBAT/Files/BestPractices/V2/$case/assembly.fa.gz
wget https://portal.nersc.gov/dna/RD/Metagenome_RD/MetaBAT/Files/BestPractices/V2/$case/depth.txt
cd ..
mv $case.tmp $case
fi
# default, minus abundance table
bins_noa=$binPrefix-$case-noabd
if [ ! -d $bins_noa ]
then
rm -rf $bins_noa.tmp
$mb2 -i $case/assembly.fa.gz -o $bins_noa.tmp/bin -v --seed 1 2>$bins_noa.err | tee $bins_noa.log
mv $bins_noa.tmp $bins_noa
fi
$DIR/checkBins.sh $bins_noa 2>&1 | tee $bins_noa-checkBins.log
cat $bins_noa/CheckM-perf.txt
# default
bins=$binPrefix-$case
if [ ! -d $bins ]
then
rm -rf $bins.tmp
$mb2 -i $case/assembly.fa.gz -a $case/depth.txt -o $bins.tmp/bin -v --seed 1 2>$bins.err | tee $bins.log
mv $bins.tmp $bins
fi
$DIR/checkBins.sh $bins 2>&1 | tee $bins-checkBins.log
cat $bins/CheckM-perf.txt
Rscript $DIR/benchmark.R $bins_noa $bins > CheckM-diffperf.txt.tmp
mv CheckM-diffperf.txt.tmp CheckM-diffperf-noabd.txt
echo "Completed diffperf between $bins_noa and $bins at $(date)"
cat CheckM-diffperf-noabd.txt
# default with minContig 2000
bins2=$binPrefix-$case-m2000
if [ ! -d $bins2 ]
then
rm -rf $bins2.tmp
$mb2 -i $case/assembly.fa.gz -a $case/depth.txt -o $bins2.tmp/bin -v -m 2000 --seed 1 2>$bin2.err | tee $bins2.log
mv $bins2.tmp $bins2
fi
$DIR/checkBins.sh $bins2 2>&1 | tee $bins2-checkBins.log
cat $bins2/CheckM-perf.txt
Rscript $DIR/benchmark.R $bins $bins2 > CheckM-diffperf.txt.tmp
mv CheckM-diffperf.txt.tmp CheckM-diffperf.txt
echo "Completed diffperf between $bins and $bins2 at $(date)"
done
trap "" 0
echo "Done with $invokedas at $(date)"
|
