sbatch mod

notebooks/slurm_scripts/launch_BWA.slurm

@@ -3,35 +3,33 @@
 #SBATCH --job-name=BWA
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
-#SBATCH --time=6:00:00
 #SBATCH --output=BWA.o
 #SBATCH --error=BWA.e
-#SBATCH --qos=6hours
 
 ### 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
-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
-singularity exec 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 container.img samtools view -bhu ERR760779_2U.sam > ERR760779_2U.bam
+singularity exec /home/container.img samtools view -bhu ERR760779_paired.sam > ERR760779_paired.bam
+singularity exec /home/container.img samtools view -bhu ERR760779_1U.sam > ERR760779_1U.bam
+singularity exec /home/container.img samtools view -bhu ERR760779_2U.sam > ERR760779_2U.bam
 
 ### sort the BAM file by position
-singularity exec 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_paired.bam > ERR760779.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
 
 ### 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
 
 ### 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
-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

notebooks/slurm_scripts/launch_MarkDuplicates.slurm

@@ -3,9 +3,5 @@
 #SBATCH --job-name=MarkDuplicates
 #SBATCH --cpus-per-task=1
 #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

notebooks/slurm_scripts/launch_bamqc.slurm

@@ -3,9 +3,5 @@
 #SBATCH --job-name=bamQC
 #SBATCH --cpus-per-task=1
 #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

notebooks/slurm_scripts/launch_fastqc.slurm

@@ -3,9 +3,5 @@
 #SBATCH --job-name=fastQC
 #SBATCH --cpus-per-task=1
 #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  .

notebooks/slurm_scripts/launch_fastqc_on_trimmed_data.slurm

@@ -3,9 +3,5 @@
 #SBATCH --job-name=fastqc_trim
 #SBATCH --cpus-per-task=1
 #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 .

notebooks/slurm_scripts/launch_index.slurm

@@ -3,9 +3,5 @@
 #SBATCH --job-name=index
 #SBATCH --cpus-per-task=1
 #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

notebooks/slurm_scripts/launch_mpileup.slurm

@@ -3,10 +3,6 @@
 #SBATCH --job-name=mpileup
 #SBATCH --cpus-per-task=1
 #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
 

notebooks/slurm_scripts/launch_snpeff.slurm

@@ -3,9 +3,5 @@
 #SBATCH --job-name=snpeff
 #SBATCH --cpus-per-task=1
 #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

notebooks/slurm_scripts/launch_trimmomatic.slurm

@@ -3,10 +3,9 @@
 #SBATCH --job-name=trimmomatic
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
-#SBATCH --time=0:30:00
 #SBATCH --output=trimmomatic.o
 #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
 

notebooks/slurm_scripts/launch_varscan.slurm

@@ -3,18 +3,17 @@
 #SBATCH --job-name=varscan
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
-#SBATCH --time=6:00:00
 #SBATCH --output=varscan.o
 #SBATCH --error=varscan.e
-#SBATCH --qos=6hours
+
 
 ### 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:
 
-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:
 
-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