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OLIVIA LANG
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add PBS scripts for simulating sid yeast
The set of yeast simulation PBS job submission scripts are added here with some walltime adjustements specific to sequencing "depth."
1 parent 3f19af8 commit 1a579c0

12 files changed

Lines changed: 397 additions & 1 deletion

‎paper/SyntheticStrain/job/run_depth_CEN.PK2-1Ca_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=00:05:00
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#PBS -A open
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#PBS -o logs/depth.CENPK.1M.log.out
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#PBS -e logs/depth.CENPK.1M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "2q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_CEN.PK2-1Ca_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.CENPK.2M.log.out
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#PBS -e logs/depth.CENPK.2M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "3q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_CEN.PK2-1Ca_3M.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.CENPK.3M.log.out
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#PBS -e logs/depth.CENPK.3M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "4q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_CEN.PK2-1Ca_4M.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=00:15:00
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#PBS -A open
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#PBS -o logs/depth.CENPK.4M.log.out
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#PBS -e logs/depth.CENPK.4M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "5q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_CEN.PK2-1Ca_500K.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=00:30:00
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#PBS -l walltime=00:05:00
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#PBS -A open
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#PBS -o logs/depth.CENPK.500K.log.out
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#PBS -e logs/depth.CENPK.500K.log.err

‎paper/SyntheticStrain/job/run_depth_CEN.PK2-1Ca_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=00:30:00
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#PBS -A open
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#PBS -o logs/depth.CENPK.5M.log.out
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#PBS -e logs/depth.CENPK.5M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "6q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_RM11-1A_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=00:05:00
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#PBS -A open
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#PBS -o logs/depth.RM11-1A.1M.log.out
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#PBS -e logs/depth.RM11-1A.1M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "8q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_RM11-1A_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.RM11-1A.2M.log.out
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#PBS -e logs/depth.RM11-1A.2M.log.err
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#PBS -t 1-100
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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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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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INFO=`sed "9q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_RM11-1A_3M.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.RM11-1A.3M.log.out
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#PBS -e logs/depth.RM11-1A.3M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "10q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

‎paper/SyntheticStrain/job/run_depth_RM11-1A_4M.pbs‎

Lines changed: 36 additions & 0 deletions
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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=00:15:00
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#PBS -A open
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#PBS -o logs/depth.RM11-1A.4M.log.out
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#PBS -e logs/depth.RM11-1A.4M.log.err
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#PBS -t 1-1000
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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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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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INFO=`sed "11q;d" depth_simulations.txt`
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STRAIN=`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=`awk -F"_" '{print $1}' <(echo $STRAIN)`
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GENOME=synthetic_genome/$STRAIN.fa
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OUTPUT=results/$STRAIN\_$DEPTH
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SEED=$(($BASE+$PBS_ARRAYID))
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start=`date +%s`
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bash ../scripts/simulate.sh -i $PBS_ARRAYID -d $DEPTH -s $SEED -g $GENOME -o $OUTPUT
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bash ../scripts/align.sh -i $PBS_ARRAYID -g ../input/$REF.fa -o $OUTPUT -t 4
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end=`date +%s`
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runtime=$((end-start))
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echo "${STRAIN} ${DEPTH} simulate in ${runtime}"

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