CITP_diversity/07_index_ref.srun at main · phillips-lab/CITP_diversity · GitHub

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#!/bin/bash
#SBATCH -A phillipslab
#SBATCH --partition=phillips       ### Partition
#SBATCH --job-name=index    ### Job Name
#SBATCH --time=10:00:00        ### WallTime
#SBATCH --nodes=1              ### Number of Nodes
#SBATCH --ntasks=1             ### Number of tasks per array job
#SBATCH --array=0           ### Array index
#SBATCH --cpus-per-task=1            ### Number of CPU cores per task

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
module load bwa samtools


mkdir -p ../ref
cd ../ref


#wget ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/sequence/genomic/c_elegans.PRJNA13758.WS280.genomic.fa.gz
#wget ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/sequence/genomic/c_elegans.PRJNA13758.WS280.genomic_masked.fa.gz

#wget ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/sequence/genomic/c_briggsae.PRJNA10731.WS280.genomic.fa.gz
#wget ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/sequence/genomic/c_briggsae.PRJNA10731.WS280.genomic_masked.fa.gz


#wget ftp://ftp.wormbase.org/pub/wormbase/species/c_tropicalis/PRJNA53597/sequence/genomic/c_tropicalis.PRJNA53597.WS280.genomic.fa.gz
#wget ftp://ftp.wormbase.org/pub/wormbase/species/c_tropicalis/PRJNA53597/sequence/genomic/c_tropicalis.PRJNA53597.WS280.genomic_masked.fa.gz

#gunzip *

ref_CE="/projects/phillipslab/ateterina/CITP_pi/ref/c_elegans.PRJNA13758.WS280.genomic.fa"
ref_CB="/projects/phillipslab/ateterina/CITP_pi/ref/c_briggsae.PRJNA10731.WS280.genomic.fa"
ref_CT="/projects/phillipslab/ateterina/CITP_pi/ref/c_tropicalis.PRJNA53597.WS280.genomic.fa"

#index the reference
bwa index $ref_CE #only ones
bwa index $ref_CB
bwa index $ref_CT

samtools faidx $ref_CE
samtools faidx $ref_CB
samtools faidx $ref_CT

module load java
picard="/projects/phillipslab/ateterina/scripts/picard/build/libs/picard.jar"
java -jar $picard CreateSequenceDictionary R=$ref_CE O=${ref_CE/.fa/.dict}
java -jar $picard CreateSequenceDictionary R=$ref_CB O=${ref_CB/.fa/.dict}
java -jar $picard CreateSequenceDictionary R=$ref_CT O=${ref_CT/.fa/.dict}