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executable file
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fq_1=$1
fq_2=$2
panel=$3
out_dir=${4%/}
barcode_length=8
# Pipeline components
gtime="aux/other_tools/time-1.9/time"
calib_cons_directory="calib_cons/"
calib_cons="consensus/calib_cons"
bam_readcount_directory="aux/other_tools/bam-readcount_v0.8.0/"
bam_readcount="aux/other_tools/bam-readcount_v0.8.0/bin/bam-readcount"
bwa_directory="aux/other_tools/bwa/"
bwa="aux/other_tools/bwa/bwa"
ref="simulating/genomes/hg19.fa"
samtools="samtools"
sinvict_directory="aux/other_tools/sinvict/"
sinvict="aux/other_tools/sinvict/sinvict"
# Clustering tools and scripts
calib="./calib"
starcode_umi="aux/other_tools/starcode/starcode-umi"
starcode="aux/other_tools/starcode/starcode"
convert_starcode="aux/convert_starcode_to_cluster.sh"
rainbow="aux/other_tools/rainbow/rainbow"
run_rainbow="aux/run_rainbow.sh"
convert_rainbow="aux/convert_rainbow_to_cluster.sh"
run_umitools="aux/run_umitools.sh"
convert_umitools="aux/convert_umitools_to_cluster.sh"
restore_cluster_missing_reads="aux/restore_cluster_missing_reads.sh"
# Plotting
run_plotting="slurm_scripts/real_tests_plotting.py"
verified_snv="experiments/real_tests/SNV.on_panel.verified.hg19.tsv"
reported_snv="experiments/real_tests/SNV.on_panel.reported.hg19.tsv"
./benchmark starcode rainbow umitools bwa calib $gtime
make -C $calib_cons_directory
make -C $bwa_directory
make -C $bam_readcount_directory
make -C $sinvict_directory
if [ ! -f $ref ]; then
echo "Reference not found. Downloading..."
wget 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz' -O chromFa.tar.gz
tar xvzfO chromFa.tar.gz > $ref
rm chromFa.tar.gz
fi
if [ ! -f "$ref.bwt" ]; then
echo "Reference BWT index is not there. Indexing..."
$bwa index $ref
fi
last_job_id=""
deps=""
mkdir -p $out_dir
for tool in umitools calib starcode rainbow raw
do
# Slurm header
echo "Preparing things for $tool"
echo "#!/bin/bash" > "$out_dir/$tool.pbs"
echo "#SBATCH --job-name=$tool" >> "$out_dir/$tool.pbs"
echo "#SBATCH -c 32" >> "$out_dir/$tool.pbs"
echo "#SBATCH --mem 512G" >> "$out_dir/$tool.pbs"
echo "#SBATCH -t 23:59:59" >> "$out_dir/$tool.pbs"
echo "#SBATCH --output=$out_dir/$tool.pbs.out" >> "$out_dir/$tool.pbs"
echo "#SBATCH --error=$out_dir/$tool.pbs.err" >> "$out_dir/$tool.pbs"
echo "#SBATCH --export=all" >> "$out_dir/$tool.pbs"
echo "#SBATCH -p debug,express,normal,big-mem,long" >> "$out_dir/$tool.pbs"
echo "touch $out_dir/$tool.pbs.no_success" >> "$out_dir/$tool.pbs"
# Tool specific commands
case $tool in
"calib")
echo "$gtime -o $out_dir/calib.gtime -v \\" >> "$out_dir/$tool.pbs"
echo " $calib \\" >> "$out_dir/$tool.pbs"
echo " -f $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " -r $fq_2 \\" >> "$out_dir/$tool.pbs"
echo " -o $out_dir/calib. \\" >> "$out_dir/$tool.pbs"
echo " -l $barcode_length \\" >> "$out_dir/$tool.pbs"
echo " --no-sort" >> "$out_dir/$tool.pbs"
;;
"starcode")
echo "$gtime -o $out_dir/starcode.gtime -v \\" >> "$out_dir/$tool.pbs"
echo " $starcode_umi \\" >> "$out_dir/$tool.pbs"
echo " --starcode-path $starcode \\" >> "$out_dir/$tool.pbs"
echo " --umi-len $barcode_length \\" >> "$out_dir/$tool.pbs"
echo " --seq-trim 50 \\" >> "$out_dir/$tool.pbs"
echo " --umi-d 2 \\" >> "$out_dir/$tool.pbs"
echo " --seq-d 5 \\" >> "$out_dir/$tool.pbs"
echo " --umi-cluster-ratio 1 \\" >> "$out_dir/$tool.pbs"
echo " --seq-cluster-ratio 1 \\" >> "$out_dir/$tool.pbs"
echo " --seq-id \\" >> "$out_dir/$tool.pbs"
echo " $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " $fq_2 \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/starcode.out" >> "$out_dir/$tool.pbs"
echo "$convert_starcode \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/starcode.out \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/starcode.cluster.temp" >> "$out_dir/$tool.pbs"
echo "$restore_cluster_missing_reads \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/starcode.cluster.temp \\" >> "$out_dir/$tool.pbs"
echo " $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/starcode.cluster" >> "$out_dir/$tool.pbs"
;;
"rainbow")
echo "$gtime -o $out_dir/rainbow.gtime -v \\" >> "$out_dir/$tool.pbs"
echo " $run_rainbow \\" >> "$out_dir/$tool.pbs"
echo " $rainbow \\" >> "$out_dir/$tool.pbs"
echo " $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " $fq_2 \\" >> "$out_dir/$tool.pbs"
echo " 2 \\" >> "$out_dir/$tool.pbs"
echo " true \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/rainbow.out" >> "$out_dir/$tool.pbs"
echo "$convert_rainbow \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/rainbow.out \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/rainbow.cluster.temp" >> "$out_dir/$tool.pbs"
echo "$restore_cluster_missing_reads \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/rainbow.cluster.temp \\" >> "$out_dir/$tool.pbs"
echo " $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/rainbow.cluster" >> "$out_dir/$tool.pbs"
;;
"umitools")
echo "$gtime -o $out_dir/umitools.gtime -v \\" >> "$out_dir/$tool.pbs"
echo " $run_umitools \\" >> "$out_dir/$tool.pbs"
echo " $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " $fq_2 \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/umitools.out \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/umitools.work \\" >> "$out_dir/$tool.pbs"
echo " $bwa \\" >> "$out_dir/$tool.pbs"
echo " $ref \\" >> "$out_dir/$tool.pbs"
echo " $samtools" >> "$out_dir/$tool.pbs"
echo "$convert_umitools \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/umitools.out \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/umitools.cluster.temp" >> "$out_dir/$tool.pbs"
echo "$restore_cluster_missing_reads \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/umitools.cluster.temp \\" >> "$out_dir/$tool.pbs"
echo " $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/umitools.cluster" >> "$out_dir/$tool.pbs"
;;
esac
# Consensus, mapping, and SNV calling
if [ $tool == "raw" ]
then
echo "cp $fq_1 $out_dir/$tool.1.fastq" >> "$out_dir/$tool.pbs"
echo "cp $fq_2 $out_dir/$tool.2.fastq" >> "$out_dir/$tool.pbs"
sinvict_depth=55
else
echo "$calib_cons \\" >> "$out_dir/$tool.pbs"
echo " -c $out_dir/$tool.cluster \\" >> "$out_dir/$tool.pbs"
echo " -q \\" >> "$out_dir/$tool.pbs"
echo " $fq_1 \\" >> "$out_dir/$tool.pbs"
echo " $fq_2 \\" >> "$out_dir/$tool.pbs"
echo " -o \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/$tool.1 \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/$tool.2 \\" >> "$out_dir/$tool.pbs"
echo " -t 8" >> "$out_dir/$tool.pbs"
sinvict_depth=3
fi
echo "$bwa mem \\" >> "$out_dir/$tool.pbs"
echo " -t 32 \\" >> "$out_dir/$tool.pbs"
echo " $ref \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/$tool.1.fastq \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/$tool.2.fastq \\" >> "$out_dir/$tool.pbs"
echo " | $samtools sort \\" >> "$out_dir/$tool.pbs"
echo " - \\" >> "$out_dir/$tool.pbs"
echo " -O BAM \\" >> "$out_dir/$tool.pbs"
echo " -@ 32 \\" >> "$out_dir/$tool.pbs"
echo " -m 2G \\" >> "$out_dir/$tool.pbs"
echo " -o $out_dir/$tool.bam" >> "$out_dir/$tool.pbs"
echo "$samtools index \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/$tool.bam" >> "$out_dir/$tool.pbs"
echo "mkdir -p $out_dir/$tool.bam-readcount" >> "$out_dir/$tool.pbs"
echo "$bam_readcount \\" >> "$out_dir/$tool.pbs"
echo " -l $panel \\" >> "$out_dir/$tool.pbs"
echo " -f $ref \\" >> "$out_dir/$tool.pbs"
echo " -w 1 \\" >> "$out_dir/$tool.pbs"
echo " $out_dir/$tool.bam \\" >> "$out_dir/$tool.pbs"
echo " > $out_dir/$tool.bam-readcount/out.tsv" >> "$out_dir/$tool.pbs"
for seq_err in 0.01 0.001 0.0001
do
echo "mkdir -p $out_dir/$tool.sinvict/$seq_err" >> "$out_dir/$tool.pbs"
echo "$sinvict \\" >> "$out_dir/$tool.pbs"
echo " -5 1 \\" >> "$out_dir/$tool.pbs"
echo " -e $seq_err \\" >> "$out_dir/$tool.pbs"
echo " -m $sinvict_depth \\" >> "$out_dir/$tool.pbs"
echo " -t $out_dir/$tool.bam-readcount \\" >> "$out_dir/$tool.pbs"
echo " -o $out_dir/$tool.sinvict/$seq_err" >> "$out_dir/$tool.pbs"
done
echo -e "rm $out_dir/$tool.pbs.no_success" >> "$out_dir/$tool.pbs"
last_job_id=$(sbatch "$out_dir/$tool.pbs")
deps=$deps":"${last_job_id##* }
done
echo "Preparing things for plotting"
echo "#!/bin/bash" > "$out_dir/plotting.pbs"
echo "#SBATCH --job-name=real_tests_plotting" >> "$out_dir/plotting.pbs"
echo "#SBATCH -c 1" >> "$out_dir/plotting.pbs"
echo "#SBATCH --mem 16G" >> "$out_dir/plotting.pbs"
echo "#SBATCH -t 02:59:59" >> "$out_dir/plotting.pbs"
echo "#SBATCH --output=$out_dir/plotting.pbs.out" >> "$out_dir/plotting.pbs"
echo "#SBATCH --error=$out_dir/plotting.pbs.err" >> "$out_dir/plotting.pbs"
echo "#SBATCH --export=all" >> "$out_dir/plotting.pbs"
echo "#SBATCH -p debug,express,normal,big-mem,long" >> "$out_dir/plotting.pbs"
echo "#SBATCH --dependency=afterany$deps" >> "$out_dir/plotting.pbs"
echo "$run_plotting $out_dir $verified_snv $reported_snv" >> "$out_dir/plotting.pbs"
sbatch "$out_dir/plotting.pbs"