diff --git a/notebooks/slurm_scripts/launch_BWA.slurm b/notebooks/slurm_scripts/launch_BWA.slurm index 66bcc10311e63518f412915debbb94ef102e76e6..6fd419ba9bcfa41591ca5d8eb5a0705de9ab7b59 100644 --- a/notebooks/slurm_scripts/launch_BWA.slurm +++ b/notebooks/slurm_scripts/launch_BWA.slurm @@ -13,7 +13,7 @@ singularity exec /home/container.img bwa mem -M ~/Workshop_SA/notebooks/referenc 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_refe/home/rence.fasta ERR760779_2U.trimmed.fastq.gz > ERR760779_2U.sam +singularity exec /home/container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_2U.trimmed.fastq.gz > ERR760779_2U.sam ### convert the SAM to BAM format singularity exec /home/container.img samtools view -bhu ERR760779_paired.sam > ERR760779_paired.bam @@ -23,7 +23,7 @@ singularity exec /home/container.img samtools view -bhu ERR760779_2U.sam > ERR76 ### sort the BAM file by position 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 +singularity exec /home/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 diff --git a/notebooks/slurm_scripts/launch_bamqc.slurm b/notebooks/slurm_scripts/launch_bamqc.slurm index 5c111ddeee027d290062f1da45e941439cd4d5e0..434c173131b3401021f29a7f3ed72fff557628f8 100644 --- a/notebooks/slurm_scripts/launch_bamqc.slurm +++ b/notebooks/slurm_scripts/launch_bamqc.slurm @@ -2,6 +2,6 @@ #SBATCH --job-name=bamQC #SBATCH --cpus-per-task=1 -#SBATCH --mem-per-cpu=2G +#SBATCH --mem-per-cpu=4G 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_snpeff.slurm b/notebooks/slurm_scripts/launch_snpeff.slurm index 18eb545eedb59af13c1b7484c75a4c31c33a667d..a311d49aef51b530d486946cad4e1097fe4cd526 100644 --- a/notebooks/slurm_scripts/launch_snpeff.slurm +++ b/notebooks/slurm_scripts/launch_snpeff.slurm @@ -4,4 +4,4 @@ #SBATCH --cpus-per-task=1 #SBATCH --mem-per-cpu=4G -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 +singularity exec /home/container.img snpEff ann -c /home/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 450100b0a2d89f11f1d03e2741947ce6d4b410af..aae38ae7d68868f48ac58e3309fedc24e66f4e7d 100644 --- a/notebooks/slurm_scripts/launch_trimmomatic.slurm +++ b/notebooks/slurm_scripts/launch_trimmomatic.slurm @@ -1,11 +1,11 @@ #!/bin/bash #SBATCH --job-name=trimmomatic -#SBATCH --cpus-per-task=1 +#SBATCH --cpus-per-task=2 #SBATCH --mem-per-cpu=4G #SBATCH --output=trimmomatic.o #SBATCH --error=trimmomatic.e -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 +singularity exec /home/container.img trimmomatic PE -phred33 -threads 2 $HOME/Workshop_SA/data_Eldholm/ERR760779_1.fastq.gz $HOME/Workshop_SA/data_Eldholm/ERR760779_2.fastq.gz ERR760779_1P.trimmed.fastq.gz ERR760779_1U.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz ERR760779_2U.trimmed.fastq.gz ILLUMINACLIP:$HOME/Workshop_SA/notebooks/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:20