diff --git a/notebooks/slurm_scripts/launch_BWA.slurm b/notebooks/slurm_scripts/launch_BWA.slurm index 8e4e0cb163115e6280f455150a62fb921e90feb6..66bcc10311e63518f412915debbb94ef102e76e6 100644 --- a/notebooks/slurm_scripts/launch_BWA.slurm +++ b/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 diff --git a/notebooks/slurm_scripts/launch_MarkDuplicates.slurm b/notebooks/slurm_scripts/launch_MarkDuplicates.slurm index cbc01bb78ae730a7abad6f6535498737e144460d..1b457fc9213cefe0f29a5389cab1d57c990200ab 100644 --- a/notebooks/slurm_scripts/launch_MarkDuplicates.slurm +++ b/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 diff --git a/notebooks/slurm_scripts/launch_bamqc.slurm b/notebooks/slurm_scripts/launch_bamqc.slurm index 8444b6cd72a93636d46fb225ce05d512aa76119a..5c111ddeee027d290062f1da45e941439cd4d5e0 100644 --- a/notebooks/slurm_scripts/launch_bamqc.slurm +++ b/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 diff --git a/notebooks/slurm_scripts/launch_fastqc.slurm b/notebooks/slurm_scripts/launch_fastqc.slurm index b294557cfed3eca46de9eb397f1f8af365c6a9e8..b3e6b0919e0cdb1ef3c2e63a1603f40904d600ea 100644 --- a/notebooks/slurm_scripts/launch_fastqc.slurm +++ b/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 . diff --git a/notebooks/slurm_scripts/launch_fastqc_on_trimmed_data.slurm b/notebooks/slurm_scripts/launch_fastqc_on_trimmed_data.slurm index c23e43b0b111ae1a5dc12c86cdb6a229cf9dc667..9a3077301eca2f3e1c6fa1c876aeced2ae950001 100644 --- a/notebooks/slurm_scripts/launch_fastqc_on_trimmed_data.slurm +++ b/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 . diff --git a/notebooks/slurm_scripts/launch_index.slurm b/notebooks/slurm_scripts/launch_index.slurm index 06e69ee46f1a55c31a785823b6e09fa35f4ec569..08f207f69227024c85a7cdd43e61172b8985e66a 100644 --- a/notebooks/slurm_scripts/launch_index.slurm +++ b/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 diff --git a/notebooks/slurm_scripts/launch_mpileup.slurm b/notebooks/slurm_scripts/launch_mpileup.slurm index 35b6e8caf16fa89be4f8eaf684818278f5040db8..d737accc19399e483851c7fdad071fd3d8323e6a 100644 --- a/notebooks/slurm_scripts/launch_mpileup.slurm +++ b/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 diff --git a/notebooks/slurm_scripts/launch_snpeff.slurm b/notebooks/slurm_scripts/launch_snpeff.slurm index d8642e264fcd05458f6658cf41731b72a32556b7..18eb545eedb59af13c1b7484c75a4c31c33a667d 100644 --- a/notebooks/slurm_scripts/launch_snpeff.slurm +++ b/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 diff --git a/notebooks/slurm_scripts/launch_trimmomatic.slurm b/notebooks/slurm_scripts/launch_trimmomatic.slurm index db616b5b444333370289fc7f5d98f847c38e9104..450100b0a2d89f11f1d03e2741947ce6d4b410af 100644 --- a/notebooks/slurm_scripts/launch_trimmomatic.slurm +++ b/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 diff --git a/notebooks/slurm_scripts/launch_varscan.slurm b/notebooks/slurm_scripts/launch_varscan.slurm index 3d547931d85cb56ff3454a8bca1d9695f45290e1..616cb273330de3f5d85c261c47233a21cc62b60d 100644 --- a/notebooks/slurm_scripts/launch_varscan.slurm +++ b/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