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Commit 0ba0fa1a authored by Chloe Marie Loiseau's avatar Chloe Marie Loiseau
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sbatch mod

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...@@ -3,35 +3,33 @@ ...@@ -3,35 +3,33 @@
#SBATCH --job-name=BWA #SBATCH --job-name=BWA
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=6:00:00
#SBATCH --output=BWA.o #SBATCH --output=BWA.o
#SBATCH --error=BWA.e #SBATCH --error=BWA.e
#SBATCH --qos=6hours
### 3.1.1 Making the index ### 3.1.1 Making the index
singularity exec container.img bwa index -a bwtsw ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta singularity exec /home/container.img bwa index -a bwtsw ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta
### 3.1.2 Running BWA ### 3.1.2 Running BWA
singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1P.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz > ERR760779_paired.sam singularity exec /home/container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1P.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz > ERR760779_paired.sam
singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1U.trimmed.fastq.gz > ERR760779_1U.sam singularity exec /home/container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1U.trimmed.fastq.gz > ERR760779_1U.sam
singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_2U.trimmed.fastq.gz > ERR760779_2U.sam singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_refe/home/rence.fasta ERR760779_2U.trimmed.fastq.gz > ERR760779_2U.sam
### convert the SAM to BAM format ### convert the SAM to BAM format
singularity exec container.img samtools view -bhu ERR760779_paired.sam > ERR760779_paired.bam singularity exec /home/container.img samtools view -bhu ERR760779_paired.sam > ERR760779_paired.bam
singularity exec container.img samtools view -bhu ERR760779_1U.sam > ERR760779_1U.bam singularity exec /home/container.img samtools view -bhu ERR760779_1U.sam > ERR760779_1U.bam
singularity exec container.img samtools view -bhu ERR760779_2U.sam > ERR760779_2U.bam singularity exec /home/container.img samtools view -bhu ERR760779_2U.sam > ERR760779_2U.bam
### sort the BAM file by position ### sort the BAM file by position
singularity exec container.img samtools sort -m 4G ERR760779_paired.bam > ERR760779.sorted.bam singularity exec /home/container.img samtools sort -m 4G ERR760779_paired.bam > ERR760779.sorted.bam
singularity exec container.img samtools sort -m 4G ERR760779_1U.bam > ERR760779_1U.sorted.bam singularity exec /home/container.img samtools sort -m 4G ERR760779_1U.bam > ERR760779_1U.sorted.bam
singularity exec container.img samtools sort -m 4G ERR760779_2U.bam > ERR760779_2U.sorted.bam singularity exec container.img samtools sort -m 4G ERR760779_2U.bam > ERR760779_2U.sorted.bam
### To go faster one could bring the three last commands into one using pipe: ### To go faster one could bring the three last commands into one using pipe:
### bwa mem -t 2 -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1P.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz | samtools view -Sbhu -|samtools sort -m 4G - ERR760779_paired.sorted ### bwa mem -t 2 -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1P.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz | samtools view -Sbhu -|samtools sort -m 4G - ERR760779_paired.sorted
### 3.1.3 Merging the BAMs ### 3.1.3 Merging the BAMs
singularity exec container.img samtools merge ERR760779_merged.bam ERR760779.sorted.bam ERR760779_1U.sorted.bam ERR760779_2U.sorted.bam singularity exec /home/container.img samtools merge ERR760779_merged.bam ERR760779.sorted.bam ERR760779_1U.sorted.bam ERR760779_2U.sorted.bam
### 3.1.4 Retrieving the unmapped reads ### 3.1.4 Retrieving the unmapped reads
singularity exec container.img samtools view -b -f 4 ERR760779_merged.bam > ERR760779.unmapped.bam singularity exec /home/container.img samtools view -b -f 4 ERR760779_merged.bam > ERR760779.unmapped.bam
...@@ -3,9 +3,5 @@ ...@@ -3,9 +3,5 @@
#SBATCH --job-name=MarkDuplicates #SBATCH --job-name=MarkDuplicates
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=6:00:00
#SBATCH --output=MarkDuplicates.o
#SBATCH --error=MarkDuplicates.e
#SBATCH --qos=6hours
singularity exec container.img picard MarkDuplicates INPUT=ERR760779_merged.bam OUTPUT=ERR760779.dedup.bam METRICS_FILE=ERR760779.markduplicates.metrics ASSUME_SORTED=true singularity exec /home/container.img picard MarkDuplicates INPUT=ERR760779_merged.bam OUTPUT=ERR760779.dedup.bam METRICS_FILE=ERR760779.markduplicates.metrics ASSUME_SORTED=true
...@@ -3,9 +3,5 @@ ...@@ -3,9 +3,5 @@
#SBATCH --job-name=bamQC #SBATCH --job-name=bamQC
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2G #SBATCH --mem-per-cpu=2G
#SBATCH --time=0:30:00
#SBATCH --output=bamQC.o
#SBATCH --error=bamQC.e
#SBATCH --qos=30min
singularity exec container.img qualimap bamqc -bam ERR760779.dedup.bam -sd -sdmode 1 -outdir . -outfile ERR760779_bamqc singularity exec /home/container.img qualimap bamqc -bam ERR760779.dedup.bam -sd -sdmode 1 -outdir . -outfile ERR760779_bamqc
...@@ -3,9 +3,5 @@ ...@@ -3,9 +3,5 @@
#SBATCH --job-name=fastQC #SBATCH --job-name=fastQC
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=0:30:00
#SBATCH --output=fastqc.o
#SBATCH --error=fastqc.e
#SBATCH --qos=30min
singularity exec container.img fastqc -q ~/Workshop_SA/data_Eldholm/ERR760779_1.fastq.gz -o . singularity exec /home/container.img fastqc -q ~/Workshop_SA/data_Eldholm/ERR760779_1.fastq.gz -o .
...@@ -3,9 +3,5 @@ ...@@ -3,9 +3,5 @@
#SBATCH --job-name=fastqc_trim #SBATCH --job-name=fastqc_trim
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=0:30:00
#SBATCH --output=fastqc_trimmed.o
#SBATCH --error=fastqc_trimmed.e
#SBATCH --qos=30min
singularity exec container.img fastqc -t 1 -q ERR760779_1P.trimmed.fastq.gz -o . singularity exec /home/container.img fastqc -t 1 -q ERR760779_1P.trimmed.fastq.gz -o .
...@@ -3,9 +3,5 @@ ...@@ -3,9 +3,5 @@
#SBATCH --job-name=index #SBATCH --job-name=index
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2G #SBATCH --mem-per-cpu=2G
#SBATCH --time=0:30:00
#SBATCH --output=index.o
#SBATCH --error=index.e
#SBATCH --qos=30min
singularity exec container.img samtools index ERR760779.dedup.bam singularity exec /home/container.img samtools index ERR760779.dedup.bam
...@@ -3,10 +3,6 @@ ...@@ -3,10 +3,6 @@
#SBATCH --job-name=mpileup #SBATCH --job-name=mpileup
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=0:30:00
#SBATCH --output=mpileup.o
#SBATCH --error=mpileup.e
#SBATCH --qos=30min
singularity exec container.img samtools mpileup -ABQ0 -q 20 -f ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779.dedup.bam > ERR760779.pileup singularity exec /home/container.img samtools mpileup -ABQ0 -q 20 -f ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779.dedup.bam > ERR760779.pileup
...@@ -3,9 +3,5 @@ ...@@ -3,9 +3,5 @@
#SBATCH --job-name=snpeff #SBATCH --job-name=snpeff
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=6:00:00
#SBATCH --output=snpeff.o
#SBATCH --error=snpeff.e
#SBATCH --qos=6hours
singularity exec container.img snpEff ann -c ~/Workshop_SA/notebooks/annotation/snpEff.config -noStats -no-downstream -no-upstream MTB_ANC -interval ~/Workshop_SA/notebooks/annotation/additionnal_annotations.bed ERR760779.snps.vcf > ERR760779.snps.ann.vcf singularity exec /home/container.img snpEff ann -c ~/Workshop_SA/notebooks/annotation/snpEff.config -noStats -no-downstream -no-upstream MTB_ANC -interval ~/Workshop_SA/notebooks/annotation/additionnal_annotations.bed ERR760779.snps.vcf > ERR760779.snps.ann.vcf
...@@ -3,10 +3,9 @@ ...@@ -3,10 +3,9 @@
#SBATCH --job-name=trimmomatic #SBATCH --job-name=trimmomatic
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=0:30:00
#SBATCH --output=trimmomatic.o #SBATCH --output=trimmomatic.o
#SBATCH --error=trimmomatic.e #SBATCH --error=trimmomatic.e
#SBATCH --qos=30min
singularity exec container.img trimmomatic PE -phred33 ~/Workshop_SA/data_Eldholm/ERR760779_1.fastq.gz ~/Workshop_SA/data_Eldholm/ERR760779_2.fastq.gz ERR760779_1P.trimmed.fastq.gz ERR760779_1U.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz ERR760779_2U.trimmed.fastq.gz ILLUMINACLIP:~/Workshop_SA/notebooks/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:20
singularity exec /home/container.img trimmomatic PE -phred33 ~/Workshop_SA/data_Eldholm/ERR760779_1.fastq.gz ~/Workshop_SA/data_Eldholm/ERR760779_2.fastq.gz ERR760779_1P.trimmed.fastq.gz ERR760779_1U.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz ERR760779_2U.trimmed.fastq.gz ILLUMINACLIP:~/Workshop_SA/notebooks/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:20
...@@ -3,18 +3,17 @@ ...@@ -3,18 +3,17 @@
#SBATCH --job-name=varscan #SBATCH --job-name=varscan
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G #SBATCH --mem-per-cpu=4G
#SBATCH --time=6:00:00
#SBATCH --output=varscan.o #SBATCH --output=varscan.o
#SBATCH --error=varscan.e #SBATCH --error=varscan.e
#SBATCH --qos=6hours
### Make Consensus calls: ### Make Consensus calls:
singularity exec container.img varscan mpileup2cns ERR760779.pileup --min-coverage 7 --min-avg-qual 20 --min-var-freq 0.1 --min-freq-for-hom 0.9 --strand-filter 1 --output-vcf 1 1> ERR760779.all.pos.vcf singularity exec /home/container.img varscan mpileup2cns ERR760779.pileup --min-coverage 7 --min-avg-qual 20 --min-var-freq 0.1 --min-freq-for-hom 0.9 --strand-filter 1 --output-vcf 1 1> ERR760779.all.pos.vcf
### Call SNPs: ### Call SNPs:
singularity exec container.img varscan mpileup2snp ERR760779.pileup --min-coverage 7 --min-avg-qual 20 --min-var-freq 0.1 --min-freq-for-hom 0.9 --strand-filter 1 --output-vcf 1 1> ERR760779.snps.vcf singularity exec /home/container.img varscan mpileup2snp ERR760779.pileup --min-coverage 7 --min-avg-qual 20 --min-var-freq 0.1 --min-freq-for-hom 0.9 --strand-filter 1 --output-vcf 1 1> ERR760779.snps.vcf
### Call InDels: ### Call InDels:
singularity exec container.img varscan mpileup2indel ERR760779.pileup --min-coverage 7 --min-avg-qual 20 --min-var-freq 0.1 --min-freq-for-hom 0.9 --strand-filter 1 --output-vcf 1 1> ERR760779.indels.vcf singularity exec /home/container.img varscan mpileup2indel ERR760779.pileup --min-coverage 7 --min-avg-qual 20 --min-var-freq 0.1 --min-freq-for-hom 0.9 --strand-filter 1 --output-vcf 1 1> ERR760779.indels.vcf
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