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add scripts to run StrainID on human simulations
These PBS scripts run StrainID on the human data simulated from K562 and HELA at the varying sequencing depths
1 parent 0ce484b commit 38dad0d

10 files changed

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‎.DS_Store‎

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‎paper/SyntheticStrain/job/run_StrainID_HELA_10M.pbs‎

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#!/bin/bash
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#PBS -l nodes=1:ppn=4
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#PBS -l pmem=16gb
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#PBS -l walltime=00:10:00
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#PBS -A open
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#PBS -o logs/depth.sid.HELA.10M.log.out
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#PBS -e logs/depth.sid.HELA.10M.log.err
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#PBS -t 1-1000
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# This script will check that 1000 BAM files have been generated before executing StrainID.
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module load gcc/8.3.1
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module load bedtools/2.27.1
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module load bwa/0.7.15
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module load samtools/1.5
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module load anaconda3
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source activate genopipe
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# FIRST CHANGE PATH TO EXECUTE
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WRK=/path/to/GenoPipe/paper/SyntheticStrain
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cd $WRK
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INFO=`sed "21q;d" depth_simulations.txt`
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LOCUS=`awk '{print $1}' <(echo $INFO)`
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DEPTH=`awk '{print $2}' <(echo $INFO)`
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BASE=`awk '{print $3}' <(echo $INFO)`
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REF=`echo $LOCUS | awk -F'_' '{print $1}'`
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SEED=$(($BASE+$PBS_ARRAYID))
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OUTPUT=$WRK/results/$LOCUS\_$DEPTH
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BAM=$WRK/results/$LOCUS\_$DEPTH/BAM/Simulation_$PBS_ARRAYID.bam
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TEMP=$WRK/temp21-$PBS_ARRAYID
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[ -d $OUTPUT/ID ] || mkdir $OUTPUT/ID
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[ -d logs ] || mkdir logs
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[ -d $TEMP ] || mkdir $TEMP
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#Check that BAM file was generated first
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if [ ! -f $BAM ];
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then
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echo "BAM input for ${LOCUS}_${DEPTH}_${PBS_ARRAYID} does not exist. Exiting."
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exit
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fi
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#Check that BAM Index file exists
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if [ ! -f $BAM.bai ];
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then
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echo "BAI missing for for ${LOCUS}_${DEPTH}_${PBS_ARRAYID}. Exiting."
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exit
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fi
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# Set-up Temp directory
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cd $TEMP
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echo $BAM
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ln -s $BAM
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ln -s $BAM.bai
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GENOME=$WRK/../input/$REF.fa
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DATABASE=$WRK/../db/$REF\_VCF
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GENOPIPE=$WRK/../..
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## Execute Single StrainID and record time
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cd $GENOPIPE/StrainID
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echo "**Begin executing StrainID for ${LOCUS}_${DEPTH}..."
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{ time bash identify-Strain.sh -i $TEMP -g $GENOME -v $DATABASE -o $OUTPUT/ID -s $SEED > $OUTPUT/ID/Simulation_$PBS_ARRAYID.std ; } 2> $OUTPUT/ID/Simulation_$PBS_ARRAYID.time
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echo "...single StrainID for ${LOCUS} ${DEPTH} finished."
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cd $WRK
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## Clean-up
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rm -r $TEMP

‎paper/SyntheticStrain/job/run_StrainID_HELA_1M.pbs‎

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#!/bin/bash
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#PBS -l nodes=1:ppn=4
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#PBS -l pmem=16gb
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#PBS -l walltime=00:10:00
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#PBS -A open
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#PBS -o logs/depth.sid.HELA.1M.log.out
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#PBS -e logs/depth.sid.HELA.1M.log.err
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#PBS -t 1-1000
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# This script will check that 1000 BAM files have been generated before executing StrainID.
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module load gcc/8.3.1
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module load bedtools/2.27.1
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module load bwa/0.7.15
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module load samtools/1.5
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module load anaconda3
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source activate genopipe
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# FIRST CHANGE PATH TO EXECUTE
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WRK=/path/to/GenoPipe/paper/SyntheticStrain
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cd $WRK
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INFO=`sed "18q;d" depth_simulations.txt`
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LOCUS=`awk '{print $1}' <(echo $INFO)`
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DEPTH=`awk '{print $2}' <(echo $INFO)`
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BASE=`awk '{print $3}' <(echo $INFO)`
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REF=`echo $LOCUS | awk -F'_' '{print $1}'`
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SEED=$(($BASE+$PBS_ARRAYID))
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OUTPUT=$WRK/results/$LOCUS\_$DEPTH
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BAM=$WRK/results/$LOCUS\_$DEPTH/BAM/Simulation_$PBS_ARRAYID.bam
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TEMP=$WRK/temp18-$PBS_ARRAYID
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[ -d $OUTPUT/ID ] || mkdir $OUTPUT/ID
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[ -d logs ] || mkdir logs
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[ -d $TEMP ] || mkdir $TEMP
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#Check that BAM file was generated first
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if [ ! -f $BAM ];
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then
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echo "BAM input for ${LOCUS}_${DEPTH}_${PBS_ARRAYID} does not exist. Exiting."
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exit
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fi
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#Check that BAM Index file exists
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if [ ! -f $BAM.bai ];
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then
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echo "BAI missing for for ${LOCUS}_${DEPTH}_${PBS_ARRAYID}. Exiting."
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exit
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fi
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# Set-up Temp directory
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cd $TEMP
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echo $BAM
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ln -s $BAM
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ln -s $BAM.bai
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GENOME=$WRK/../input/$REF.fa
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DATABASE=$WRK/../db/$REF\_VCF
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GENOPIPE=$WRK/../..
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## Execute Single StrainID and record time
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cd $GENOPIPE/StrainID
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echo "**Begin executing StrainID for ${LOCUS}_${DEPTH}..."
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{ time bash identify-Strain.sh -i $TEMP -g $GENOME -v $DATABASE -o $OUTPUT/ID -s $SEED > $OUTPUT/ID/Simulation_$PBS_ARRAYID.std ; } 2> $OUTPUT/ID/Simulation_$PBS_ARRAYID.time
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echo "...single StrainID for ${LOCUS} ${DEPTH} finished."
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cd $WRK
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## Clean-up
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rm -r $TEMP

‎paper/SyntheticStrain/job/run_StrainID_HELA_20M.pbs‎

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#!/bin/bash
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#PBS -l nodes=1:ppn=4
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#PBS -l pmem=16gb
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#PBS -l walltime=00:10:00
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#PBS -A open
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#PBS -o logs/depth.sid.HELA.20M.log.out
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#PBS -e logs/depth.sid.HELA.20M.log.err
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#PBS -t 1-1000
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# This script will check that 1000 BAM files have been generated before executing StrainID.
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module load gcc/8.3.1
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module load bedtools/2.27.1
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module load bwa/0.7.15
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module load samtools/1.5
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module load anaconda3
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source activate genopipe
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# FIRST CHANGE PATH TO EXECUTE
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WRK=/path/to/GenoPipe/paper/SyntheticStrain
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cd $WRK
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INFO=`sed "22q;d" depth_simulations.txt`
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LOCUS=`awk '{print $1}' <(echo $INFO)`
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DEPTH=`awk '{print $2}' <(echo $INFO)`
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BASE=`awk '{print $3}' <(echo $INFO)`
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REF=`echo $LOCUS | awk -F'_' '{print $1}'`
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SEED=$(($BASE+$PBS_ARRAYID))
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OUTPUT=$WRK/results/$LOCUS\_$DEPTH
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BAM=$WRK/results/$LOCUS\_$DEPTH/BAM/Simulation_$PBS_ARRAYID.bam
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TEMP=$WRK/temp22-$PBS_ARRAYID
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[ -d $OUTPUT/ID ] || mkdir $OUTPUT/ID
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[ -d logs ] || mkdir logs
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[ -d $TEMP ] || mkdir $TEMP
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#Check that BAM file was generated first
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if [ ! -f $BAM ];
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then
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echo "BAM input for ${LOCUS}_${DEPTH}_${PBS_ARRAYID} does not exist. Exiting."
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exit
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fi
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#Check that BAM Index file exists
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if [ ! -f $BAM.bai ];
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then
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echo "BAI missing for for ${LOCUS}_${DEPTH}_${PBS_ARRAYID}. Exiting."
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exit
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fi
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# Set-up Temp directory
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cd $TEMP
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echo $BAM
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ln -s $BAM
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ln -s $BAM.bai
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GENOME=$WRK/../input/$REF.fa
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DATABASE=$WRK/../db/$REF\_VCF
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GENOPIPE=$WRK/../..
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## Execute Single StrainID and record time
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cd $GENOPIPE/StrainID
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echo "**Begin executing StrainID for ${LOCUS}_${DEPTH}..."
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{ time bash identify-Strain.sh -i $TEMP -g $GENOME -v $DATABASE -o $OUTPUT/ID -s $SEED > $OUTPUT/ID/Simulation_$PBS_ARRAYID.std ; } 2> $OUTPUT/ID/Simulation_$PBS_ARRAYID.time
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echo "...single StrainID for ${LOCUS} ${DEPTH} finished."
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cd $WRK
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## Clean-up
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rm -r $TEMP

‎paper/SyntheticStrain/job/run_StrainID_HELA_2M.pbs‎

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#!/bin/bash
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#PBS -l nodes=1:ppn=4
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#PBS -l pmem=16gb
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#PBS -l walltime=00:10:00
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#PBS -A open
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#PBS -o logs/depth.sid.HELA.2M.log.out
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#PBS -e logs/depth.sid.HELA.2M.log.err
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#PBS -t 1-1000
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# This script will check that 1000 BAM files have been generated before executing StrainID.
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module load gcc/8.3.1
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module load bedtools/2.27.1
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module load bwa/0.7.15
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module load samtools/1.5
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module load anaconda3
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source activate genopipe
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# FIRST CHANGE PATH TO EXECUTE
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WRK=/path/to/GenoPipe/paper/SyntheticStrain
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cd $WRK
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INFO=`sed "19q;d" depth_simulations.txt`
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LOCUS=`awk '{print $1}' <(echo $INFO)`
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DEPTH=`awk '{print $2}' <(echo $INFO)`
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BASE=`awk '{print $3}' <(echo $INFO)`
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REF=`echo $LOCUS | awk -F'_' '{print $1}'`
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SEED=$(($BASE+$PBS_ARRAYID))
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OUTPUT=$WRK/results/$LOCUS\_$DEPTH
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BAM=$WRK/results/$LOCUS\_$DEPTH/BAM/Simulation_$PBS_ARRAYID.bam
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TEMP=$WRK/temp19-$PBS_ARRAYID
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[ -d $OUTPUT/ID ] || mkdir $OUTPUT/ID
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[ -d logs ] || mkdir logs
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[ -d $TEMP ] || mkdir $TEMP
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#Check that BAM file was generated first
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if [ ! -f $BAM ];
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then
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echo "BAM input for ${LOCUS}_${DEPTH}_${PBS_ARRAYID} does not exist. Exiting."
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exit
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fi
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#Check that BAM Index file exists
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if [ ! -f $BAM.bai ];
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then
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echo "BAI missing for for ${LOCUS}_${DEPTH}_${PBS_ARRAYID}. Exiting."
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exit
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fi
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# Set-up Temp directory
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cd $TEMP
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echo $BAM
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ln -s $BAM
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ln -s $BAM.bai
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GENOME=$WRK/../input/$REF.fa
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DATABASE=$WRK/../db/$REF\_VCF
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GENOPIPE=$WRK/../..
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## Execute Single StrainID and record time
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cd $GENOPIPE/StrainID
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echo "**Begin executing StrainID for ${LOCUS}_${DEPTH}..."
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{ time bash identify-Strain.sh -i $TEMP -g $GENOME -v $DATABASE -o $OUTPUT/ID -s $SEED > $OUTPUT/ID/Simulation_$PBS_ARRAYID.std ; } 2> $OUTPUT/ID/Simulation_$PBS_ARRAYID.time
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echo "...single StrainID for ${LOCUS} ${DEPTH} finished."
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cd $WRK
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## Clean-up
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rm -r $TEMP

‎paper/SyntheticStrain/job/run_StrainID_HELA_5M.pbs‎

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#!/bin/bash
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#PBS -l nodes=1:ppn=4
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#PBS -l pmem=16gb
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#PBS -l walltime=00:10:00
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#PBS -A open
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#PBS -o logs/depth.sid.HELA.5M.log.out
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#PBS -e logs/depth.sid.HELA.5M.log.err
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#PBS -t 1-1000
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# This script will check that 1000 BAM files have been generated before executing StrainID.
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module load gcc/8.3.1
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module load bedtools/2.27.1
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module load bwa/0.7.15
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module load samtools/1.5
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module load anaconda3
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source activate genopipe
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# FIRST CHANGE PATH TO EXECUTE
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WRK=/path/to/GenoPipe/paper/SyntheticStrain
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cd $WRK
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INFO=`sed "20q;d" depth_simulations.txt`
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LOCUS=`awk '{print $1}' <(echo $INFO)`
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DEPTH=`awk '{print $2}' <(echo $INFO)`
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BASE=`awk '{print $3}' <(echo $INFO)`
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REF=`echo $LOCUS | awk -F'_' '{print $1}'`
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SEED=$(($BASE+$PBS_ARRAYID))
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OUTPUT=$WRK/results/$LOCUS\_$DEPTH
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BAM=$WRK/results/$LOCUS\_$DEPTH/BAM/Simulation_$PBS_ARRAYID.bam
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TEMP=$WRK/temp20-$PBS_ARRAYID
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[ -d $OUTPUT/ID ] || mkdir $OUTPUT/ID
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[ -d logs ] || mkdir logs
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[ -d $TEMP ] || mkdir $TEMP
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#Check that BAM file was generated first
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if [ ! -f $BAM ];
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then
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echo "BAM input for ${LOCUS}_${DEPTH}_${PBS_ARRAYID} does not exist. Exiting."
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exit
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fi
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#Check that BAM Index file exists
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if [ ! -f $BAM.bai ];
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then
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echo "BAI missing for for ${LOCUS}_${DEPTH}_${PBS_ARRAYID}. Exiting."
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exit
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fi
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# Set-up Temp directory
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cd $TEMP
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echo $BAM
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ln -s $BAM
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ln -s $BAM.bai
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GENOME=$WRK/../input/$REF.fa
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DATABASE=$WRK/../db/$REF\_VCF
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GENOPIPE=$WRK/../..
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## Execute Single StrainID and record time
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cd $GENOPIPE/StrainID
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echo "**Begin executing StrainID for ${LOCUS}_${DEPTH}..."
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{ time bash identify-Strain.sh -i $TEMP -g $GENOME -v $DATABASE -o $OUTPUT/ID -s $SEED > $OUTPUT/ID/Simulation_$PBS_ARRAYID.std ; } 2> $OUTPUT/ID/Simulation_$PBS_ARRAYID.time
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echo "...single StrainID for ${LOCUS} ${DEPTH} finished."
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cd $WRK
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## Clean-up
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rm -r $TEMP

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