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Difference between revisions of "Applications/Ncbi-blast"

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m (→‎SLURM Script)
m (→‎Batch Script)
Line 43: Line 43:
 
#!/bin/bash
 
#!/bin/bash
  
−
fasta=/home/user1/maker.all.proteins.fasta
+
#SBATCH -J blast
−
seqs_per_file=300
 
−
files_per_dir=100
 
−
BLAST_DB=/home/user1/database/nr_metazoa
 
−
prefix=Tcancriformis_maker2
 
−
threads_per_job=28
 
−
e=1e-5
 
−
cul=10
 
−
n_seqs=50
 
−
fmt=5 #5=xml
 
−
basedir=$(pwd)
 
−
partition_script=/home/user1/ectools/partition.py
 
−
 
 
−
###########
 
−
 
 
−
echo -e "\nsplitting up files\n"
 
−
#cat $fasta | sed 's/ .*//g' > $genome.fasta
 
−
python $partition_script $seqs_per_file $files_per_dir $fasta
 
−
 
 
−
count=$(ls -1 | grep -E "^[0-9]{4}" |wc -l)
 
−
for i in $(seq $count -1 1)
 
−
do
 
−
        current=$(printf "%04d" $i)
 
−
        echo -e "processing directory $current\n"
 
−
        cd $current
 
−
 
 
−
        for p in $(ls -1 | grep -E "p[0-9]{4}$" | sort -nr)
 
−
        do
 
−
 
 
−
                echo -e "#!/bin/bash
 
−
#SBATCH -J b-$current-$p-$prefix
 
 
#SBATCH -N 1
 
#SBATCH -N 1
−
#SBATCH --ntasks-per-node $threads_per_job
+
#SBATCH --ntasks-per-node 1
 
#SBATCH -o job-%j.out
 
#SBATCH -o job-%j.out
 
#SBATCH -e job-%j.out
 
#SBATCH -e job-%j.out
 
#SBATCH -p compute
 
#SBATCH -p compute
  
−
#LOAD MODULE
+
# perfoms NR blast (blastx)
−
module add ncbi-blast/2.4.0
+
infile="$1"
−
#
+
outfile="$(basename "${infile%.*}").xml"
−
date
+
database="/swissprot/uniprot_sprot"
−
cd $basedir/$current
 
−
 
 
−
echo -e \"\\\nNumber of scaffolds to process:\\\t\$(cat $basedir/$current/${p} | grep \">\" | wc -l)\"
 
−
echo -e \"\\\nTotal length of scaffolds:\\\t\$(cat $basedir/$current/${p} | grep \">\" -v | perl -ne 'chomp; print \"\$_\"' | wc -m)\\\n\"
 
  
−
blastp -query ${p} -db $BLAST_DB -outfmt $fmt -max_target_seqs $n_seqs -culling_limit $cul -num_threads \$SLURM_NTASKS_PER_NODE -evalue $e -out ${p}-vs-nt-n$n_seqs.cul$cul.$e.blastp.out.xml
+
module purge
 +
module load ncbi-blast
  
−
echo -e \"\\\nDONE\\\n\"
+
blastp \
−
date" > run_blastn_${p}.slurm.sh
+
-query "${infile}" \
−
                sbatch run_blastn_${p}.slurm.sh
+
-db "${database}" \
−
        done
+
-out "${outfile}".xml \
−
        cd ..
+
-evalue 1e-5 \
−
done
+
-num_threads 8 \
 +
-max_target_seqs 50 \
 +
-outfmt 5
  
 
</pre>
 
</pre>

Revision as of 12:05, 17 November 2022

Application Details

  • Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
  • Version: 2.4.0 , 2.6.0
  • Modules: ncbi-blast/2.4.0, ncbi-blast/2.6.0
  • Licence: Open-source (BLAST is a registered trademark of the National Library of Medicine)

Usage Examples

Command Set

ncbi-blast provides the following commands:

  • blast_formatter
  • blastdb_aliastool
  • blastdbcheck
  • blastdbcmd
  • blastn
  • blastp
  • blastx
  • convert2blastmask
  • deltablast
  • dustmasker
  • legacy_blast.pl
  • makeblastdb
  • makembindex
  • makeprofiledb
  • psiblast
  • rpsblast
  • rpstblastn
  • segmasker
  • tblastn
  • tblastx
  • update_blastdb.pl
  • windowmasker


Batch Script


#!/bin/bash

#SBATCH -J blast
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -o job-%j.out
#SBATCH -e job-%j.out
#SBATCH -p compute

# perfoms NR blast (blastx)
infile="$1"
outfile="$(basename "${infile%.*}").xml"
database="/swissprot/uniprot_sprot"

module purge
module load ncbi-blast

blastp \
 -query "${infile}" \
 -db "${database}" \
 -out "${outfile}".xml \
 -evalue 1e-5 \
 -num_threads 8 \
 -max_target_seqs 50 \
 -outfmt 5

Further Information





Modules | Main Page | Further Topics

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