HPC

Difference between revisions of "Applications/Ncbi-blast"

From HPC
Jump to: navigation , search
m
m (→‎Batch Script)
 
(5 intermediate revisions by the same user not shown)
Line 37: Line 37:
  
  
−
===SLURM Script===
+
===Interactive Session===
  
−
<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
+
<pre style="background-color: #000; color: white; font-family: monospace, sans-serif;">
  
−
#!/bin/bash
+
[username@login01 ~]$ interactive
 +
salloc: Granted job allocation 3619736
 +
Job ID 3619736 connecting to c081, please wait...
 +
c081.vc-main
 +
[username@c081 ~]$ module add ncbi-blast/2.
 +
ncbi-blast/2.11.0  ncbi-blast/2.12.0  ncbi-blast/2.4.0  ncbi-blast/2.6.0
 +
[username@c081 ~]$ module add ncbi-blast/2.6.0
 +
[username@c081 ~] blastp <user options>
  
−
fasta=/home/user1/maker.all.proteins.fasta
+
</pre>
−
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
 
  
−
###########
+
===Batch Script===
  
−
echo -e "\nsplitting up files\n"
+
<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
−
#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)
+
#!/bin/bash
−
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 blast
−
#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)\"
+
module purge
−
echo -e \"\\\nTotal length of scaffolds:\\\t\$(cat $basedir/$current/${p} | grep \">\" -v | perl -ne 'chomp; print \"\$_\"' | wc -m)\\\n\"
+
module load ncbi-blast/2.6.0
  
−
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
+
blastp \
−
 
+
-query "${infile}" \
−
echo -e \"\\\nDONE\\\n\"
+
-db "${database}" \
−
date" > run_blastn_${p}.slurm.sh
+
-out "${outfile}".xml \
−
                sbatch run_blastn_${p}.slurm.sh
+
-evalue 1e-5 \
−
        done
+
-num_threads 8 \
−
        cd ..
+
-max_target_seqs 50 \
−
done
+
-outfmt 5
  
 
</pre>
 
</pre>
−
 
−
 
  
 
==Further Information==
 
==Further Information==
Line 106: Line 88:
 
* [https://blast.ncbi.nlm.nih.gov/Blast.cgi https://blast.ncbi.nlm.nih.gov/Blast.cgi]
 
* [https://blast.ncbi.nlm.nih.gov/Blast.cgi https://blast.ncbi.nlm.nih.gov/Blast.cgi]
  
−
==Navigation==
+
{{Modulepagenav}}
−
 
 
−
* [[Main_Page|Home]]
 
−
* [[Applications|Application support]] *
 
−
* [[General|General]]
 
−
* [[Programming|Programming support]]
 

Latest revision as of 12:11, 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


Interactive Session


[username@login01 ~]$ interactive
salloc: Granted job allocation 3619736
Job ID 3619736 connecting to c081, please wait...
c081.vc-main
[username@c081 ~]$ module add ncbi-blast/2.
ncbi-blast/2.11.0  ncbi-blast/2.12.0  ncbi-blast/2.4.0   ncbi-blast/2.6.0
[username@c081 ~]$ module add ncbi-blast/2.6.0
[username@c081 ~] blastp <user options>

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/2.6.0

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

Retrieved from ‘http://hpc.mediawiki.hull.ac.uk/index.php?title=Applications/Ncbi-blast&oldid=41212’