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slurm_maker.Rmd
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slurm_maker.Rmd
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---
title: "slurm maker"
output: html_notebook
---
#Trimmomatic
```{bash}
echo "" > submit_all_sbatch.bat
account_name=mcnamara-lab
n_core=8
memory_in_MB=64000
hours=3
adapter=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/new_align_read/TruSeq3-PE.fa
for infile in /project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/raw_data/*_1.fq.gz
do
sample_name="$(basename $infile _1.fq.gz)"
sbatch_filename=trimmo_$sample_name.slurm
message_print=trimmo_$sample_name.out
infile1=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/raw_data/"$(basename $infile _1.fq.gz)"_1.fq.gz
infile2=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/raw_data/"$(basename $infile _1.fq.gz)"_2.fq.gz
output_dir=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/new_align_read/trimmed/
outfile1=$output_dir"$(basename $infile _1.fq.gz)"_paired_1.fq.gz
outfile1_1=$output_dir"$(basename $infile _1.fq.gz)"_unpaired_1.fq.gz
outfile2=$output_dir"$(basename $infile _1.fq.gz)"_paired_2.fq.gz
outfile2_1=$output_dir"$(basename $infile _1.fq.gz)"_unpaired_2.fq.gz
echo '#!/bin/bash' > $sbatch_filename
echo "#SBATCH -n $n_core" >> $sbatch_filename
echo "#SBATCH --mem=$memory_in_MB" >> $sbatch_filename
echo "#SBATCH -t $hours:00:00" >> $sbatch_filename
echo "#SBATCH -o $message_print" >> $sbatch_filename
echo "#SBATCH -A $account_name" >> $sbatch_filename
echo "#SBATCH -p standard" >> $sbatch_filename
echo "" >> $sbatch_filename
echo 'module load trimmomatic/0.39' >> $sbatch_filename
echo "infile1=$infile1" >> $sbatch_filename
echo "infile2=$infile2" >> $sbatch_filename
echo "outfile1=$outfile1" >> $sbatch_filename
echo "outfile1_1=$outfile1_1" >> $sbatch_filename
echo "outfile2=$outfile2" >> $sbatch_filename
echo "outfile2_2=$outfile2_1" >> $sbatch_filename
echo "" >> $sbatch_filename
echo "java -jar \$EBROOTTRIMMOMATIC/trimmomatic-0.39.jar PE -phred33 -threads 8 \
$infile1 $infile2 \
$outfile1 $outfile1_1 $outfile2 $outfile2_1 \
ILLUMINACLIP:$adapter:2:30:10 LEADING:3 \
TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36" >> $sbatch_filename
echo "sbatch $sbatch_filename" >> submit_all_sbatch.bat
done
```
#STAR
```{bash}
#gz files requires 64GB
echo "" > submit_all_sbatch.bat
account_name=mcnamara-lab
n_core=8
memory_in_MB=64000
hours=3
gtffile=/project/mcnamara-lab/myles_kim/Genome_references/human/gencode.v41.primary_assembly.annotation.gtf
genomedir=/project/mcnamara-lab/myles_kim/Genome_references/human/genomeIndex_star_20221007
for infile in /project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/new_align_read/trimmed/*_paired_1.fq.gz
do
sample_name="$(basename $infile _paired_1.fq.gz)"
sbatch_filename=star_$sample_name.slurm
message_print=star_$sample_name.out
infile1=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/new_align_read/trimmed/"$(basename $infile _paired_1.fq.gz)"_paired_1.fq.gz
infile2=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/new_align_read/trimmed/"$(basename $infile _paired_1.fq.gz)"_paired_2.fq.gz
outfile=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/new_align_read/aligned_by_star/"$(basename $infile _paired_1.fq.gz)"_
echo '#!/bin/bash' > $sbatch_filename
echo "#SBATCH -n $n_core" >> $sbatch_filename
echo "#SBATCH --mem=$memory_in_MB" >> $sbatch_filename
echo "#SBATCH -t $hours:00:00" >> $sbatch_filename
echo "#SBATCH -o $message_print" >> $sbatch_filename
echo "#SBATCH -A $account_name" >> $sbatch_filename
echo "#SBATCH -p standard" >> $sbatch_filename
echo "" >> $sbatch_filename
echo 'module load star/2.7.9a' >> $sbatch_filename
echo "infile1=$infile1" >> $sbatch_filename
echo "infile2=$infile2" >> $sbatch_filename
echo "outfile=$outfile" >> $sbatch_filename
echo "STAR --genomeDir $genomedir --sjdbGTFfile $gtffile --runThreadN 8 --readFilesCommand zcat \
--readFilesIn $infile1 $infile2 --outFileNamePrefix $outfile --outSAMtype BAM SortedByCoordinate \
--outSAMunmapped None --outSAMattributes All --quantMode GeneCounts" >> $sbatch_filename
echo "sbatch $sbatch_filename" >> submit_all_sbatch.bat
done
#--outFilterMismatchNmax 3 --outFilterMultimapNmax 1
```
annot_gff=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.107.gtf
featurecount_loc=/project/mcnamara-lab/myles_kim/featurecounts_latest.sif
input_bam=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/BCCR6N16Aligned.sortedByCoord.out.bam
output_txt=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/count_BCCR6N16.txt
echo '#!/bin/bash' >> $file_name
echo '#SBATCH -p standard' >> $file_name
echo "#SBATCH -n $n_core" >> $file_name
echo "#SBATCH --mem=$memory_in_MB" >> $file_name
echo "#SBATCH -t $hours:00:00" >> $file_name
echo "#SBATCH -o $message_print" >> $file_name
echo "#SBATCH -A $account_name" >> $file_name
echo "" >> $file_name
echo "module purge" >> $file_name
echo "annot_gff=$annot_gff" >> $file_name
echo "featurecount_loc=$featurecount_loc" >> $file_name
echo "input_bam=$input_bam" >> $file_name
echo "output_txt=$output_txt" >> $file_name
echo 'singularity exec $featurecount_loc \' >> $file_name
echo 'featureCounts -T 8 -p -t gene -g gene_id -a $annot_gff -o $output_txt $input_bam' >> $file_name
#!/bin/bash
#SBATCH -n 16
#SBATCH --mem=64000
#SBATCH -t 10:00:00
#SBATCH -o star_slurm.out
#SBATCH -p standard
#SBATCH -A mcnamara-lab
module purge
annot_gff=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.107.gtf
featurecount_loc=/project/mcnamara-lab/myles_kim/featurecounts_latest.sif
input_bam=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/BCCR6N16Aligned.sortedByCoord.out.bam
output_txt=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/count_BCCR6N16.txt
singularity exec $featurecount_loc \
featureCounts -T 8 -p -t gene -g gene_id -a $annot_gff -o $output_txt $input_bam
```
```{bash}
echo "" > submit_all_sbatch.bat
#kall_index=/project/mcnamara-lab/myles_kim/Genome_references/human/gencode.v41.transcripts.idx
kall_index=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.cdna.all.idx
trimmed_fq=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/trimmed/
for infile in /project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/trimmed/*_paired_1.fq
do
sample_name="$(basename $infile _paired_1.fq)"
#mkdir $sample_name
#mkdir $sample_name/kallisto
echo $sample_name
sbatch_filename=kallisto_$sample_name.slurm
echo $sbatch_filename
n_core=8
memory_in_MB=64000
hours=3
message_print=$sample_name.out
account_name=mcnamara-lab
file1_name=$infile
file2_name=$trimmed_fq"$(basename $infile _paired_1.fq)"_paired_2.fq
out_dir=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/counts_by_kallisto/$sample_name/kallisto
annot_gtf=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.107.gtf
echo '#!/bin/bash' > $sbatch_filename
echo "#SBATCH -n $n_core" >> $sbatch_filename
echo "#SBATCH --mem=$memory_in_MB" >> $sbatch_filename
echo "#SBATCH -t $hours:00:00" >> $sbatch_filename
echo "#SBATCH -o $message_print" >> $sbatch_filename
echo "#SBATCH -A $account_name" >> $sbatch_filename
echo "#SBATCH -p standard" >> $sbatch_filename
echo "" >> $sbatch_filename
echo "module purge" >> $sbatch_filename
echo 'module load kallisto/0.46.2' >> $sbatch_filename
echo "" >> $sbatch_filename
echo "annot_gtf=$annot_gtf" >> $sbatch_filename
echo "kall_index=$kall_index" >> $sbatch_filename
echo "infile1=$file1_name" >> $sbatch_filename
echo "infile2=$file2_name" >> $sbatch_filename
echo "out_dir=$out_dir" >> $sbatch_filename
echo 'kallisto quant -b 100 --genomebam --gtf $annot_gtf -t 8 -i $kall_index -o $out_dir $infile1 $infile2' >> $sbatch_filename
#echo 'kallisto quant -b 100 -t 8 -i $kall_index -o $out_dir $infile1 $infile2' >> $sbatch_filename
#echo 'kallisto quant -b 100 --genomebam --gtf $annot_gtf -t 8 -i $kall_index -o $out_dir $infile1 $infile2' >> $sbatch_filename
# --bootstrap-samples=50
echo "sbatch $sbatch_filename" >> submit_all_sbatch.bat
done
```
```{bash}
echo "" > submit_all_sbatch.bat
memory_in_MB=32000
n_core=8
hours=10
message_print=star_slurm.out
account_name=mcnamara-lab
file_name=test_slurm.slurm
annot_gff=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.107.gtf
featurecount_loc=/project/mcnamara-lab/myles_kim/featurecounts_latest.sif
input_bam=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/BCCR6N16Aligned.sortedByCoord.out.bam
output_txt=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/count_BCCR6N16.txt
echo '#!/bin/bash' >> $file_name
echo '#SBATCH -p standard' >> $file_name
echo "#SBATCH -n $n_core" >> $file_name
echo "#SBATCH --mem=$memory_in_MB" >> $file_name
echo "#SBATCH -t $hours:00:00" >> $file_name
echo "#SBATCH -o $message_print" >> $file_name
echo "#SBATCH -A $account_name" >> $file_name
echo "" >> $file_name
echo "module purge" >> $file_name
echo "annot_gff=$annot_gff" >> $file_name
echo "featurecount_loc=$featurecount_loc" >> $file_name
echo "input_bam=$input_bam" >> $file_name
echo "output_txt=$output_txt" >> $file_name
echo 'singularity exec $featurecount_loc \' >> $file_name
echo 'featureCounts -T 8 -p -t gene -g gene_id -a $annot_gff -o $output_txt $input_bam' >> $file_name
#!/bin/bash
#SBATCH -n 16
#SBATCH --mem=64000
#SBATCH -t 10:00:00
#SBATCH -o star_slurm.out
#SBATCH -p standard
#SBATCH -A mcnamara-lab
module purge
annot_gff=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.107.gtf
featurecount_loc=/project/mcnamara-lab/myles_kim/featurecounts_latest.sif
input_bam=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/BCCR6N16Aligned.sortedByCoord.out.bam
output_txt=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/mapped_by_star/count_BCCR6N16.txt
singularity exec $featurecount_loc \
featureCounts -T 8 -p -t gene -g gene_id -a $annot_gff -o $output_txt $input_bam
```
```{bash}
echo "" > submit_all_sbatch.bat
account_name=mcnamara-lab
n_core=8
memory_in_MB=64000
hours=3
annot_gtf=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.107.gtf
htseq_loc=/project/mcnamara-lab/myles_kim/htseq_latest.sif
for infile in /project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/aligned_by_star/*.bam
do
sample_name="$(basename $infile _Aligned.sortedByCoord.out.bam)"
echo $sample_name
sbatch_filename=htseq_$sample_name.slurm
echo $sbatch_filename
message_print=$sample_name.out
out_file=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/counts_by_htseq/$sample_name.count_by_htseq.txt
echo '#!/bin/bash' > $sbatch_filename
echo "#SBATCH -n $n_core" >> $sbatch_filename
echo "#SBATCH --mem=$memory_in_MB" >> $sbatch_filename
echo "#SBATCH -t $hours:00:00" >> $sbatch_filename
echo "#SBATCH -o $message_print" >> $sbatch_filename
echo "#SBATCH -A $account_name" >> $sbatch_filename
echo "#SBATCH -p standard" >> $sbatch_filename
echo "" >> $sbatch_filename
echo "annot_gtf=$annot_gtf" >> $sbatch_filename
echo "htseq_loc=$htseq_loc" >> $sbatch_filename
echo "infile=$infile" >> $sbatch_filename
echo "out_file=$out_file" >> $sbatch_filename
echo "" >> $sbatch_filename
echo 'singularity exec $htseq_loc htseq-count -s no -t gene -i gene_id --additional-attr=gene_name $infile $annot_gtf > $out_file' >> $sbatch_filename
echo "sbatch $sbatch_filename" >> submit_all_sbatch.bat
done
#singularity exec $htseq_loc htseq-count -s no -t gene -i gene_id --additional-attr=gene_name
```
```{done}
for file in ./*
do
echo $file
if [ $file == "./test_slurm.sslurm" ]
then
echo "Number is Even"
else
echo "I am doing any."
fi
done
```
```{bash}
#Salmon
out_dir=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/counts_by_salmon/BCCR6N16
bamfile=/project/mcnamara-lab/myles_kim/CAD_v_Normal/Normal/aligned_by_star/BCCR6N16_Aligned.sortedByCoord.out.bam
#tx_fa=/project/mcnamara-lab/myles_kim/Genome_references/human/gencode.v41.transcripts.fa
tx_fa=/project/mcnamara-lab/myles_kim/Genome_references/human/Homo_sapiens.GRCh38.cdna.all.fa
salmon quant -t $tx_fa -l A -a $bamfile -o $out_dir
```