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Difference between revisions of "Applications/Ncbi-blast"

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===SLURM Script===
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===Interactive Session===
  
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
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<pre style="background-color: #000; color: white; font-family: monospace, sans-serif;">
  
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#!/bin/bash
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[username@login01 ~]$ interactive
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salloc: Granted job allocation 3619736
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Job ID 3619736 connecting to c081, please wait...
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c081.vc-main
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[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
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[username@c081 ~]$ module add ncbi-blast/2.6.0
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[username@c081 ~] blastp <user options>
  
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fasta=/home/user1/maker.all.proteins.fasta
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</pre>
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seqs_per_file=300
 
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files_per_dir=100
 
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BLAST_DB=/home/user1/database/nr_metazoa
 
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prefix=Tcancriformis_maker2
 
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threads_per_job=28
 
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e=1e-5
 
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cul=10
 
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n_seqs=50
 
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fmt=5 #5=xml
 
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basedir=$(pwd)
 
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partition_script=/home/user1/ectools/partition.py
 
  
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###########
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===Batch Script===
  
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echo -e "\nsplitting up files\n"
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
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#cat $fasta | sed 's/ .*//g' > $genome.fasta
 
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python $partition_script $seqs_per_file $files_per_dir $fasta
 
  
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count=$(ls -1 | grep -E "^[0-9]{4}" |wc -l)
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#!/bin/bash
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for i in $(seq $count -1 1)
 
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do
 
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        current=$(printf "%04d" $i)
 
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        echo -e "processing directory $current\n"
 
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        cd $current
 
  
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        for p in $(ls -1 | grep -E "p[0-9]{4}$" | sort -nr)
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#SBATCH -J blast
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        do
 
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                echo -e "#!/bin/bash
 
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#SBATCH -J b-$current-$p-$prefix
 
 
#SBATCH -N 1
 
#SBATCH -N 1
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#SBATCH --ntasks-per-node $threads_per_job
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#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
  
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#LOAD MODULE
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# perfoms NR blast (blastx)
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module add ncbi-blast/2.4.0
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infile="$1"
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#
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outfile="$(basename "${infile%.*}").xml"
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date
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database="/swissprot/uniprot_sprot"
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cd $basedir/$current
 
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echo -e \"\\\nNumber of scaffolds to process:\\\t\$(cat $basedir/$current/${p} | grep \">\" | wc -l)\"
 
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echo -e \"\\\nTotal length of scaffolds:\\\t\$(cat $basedir/$current/${p} | grep \">\" -v | perl -ne 'chomp; print \"\$_\"' | wc -m)\\\n\"
 
  
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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
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module purge
 +
module load ncbi-blast/2.6.0
  
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echo -e \"\\\nDONE\\\n\"
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blastp \
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date" > run_blastn_${p}.slurm.sh
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-query "${infile}" \
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                sbatch run_blastn_${p}.slurm.sh
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-db "${database}" \
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        done
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-out "${outfile}".xml \
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        cd ..
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-evalue 1e-5 \
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done
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-num_threads 8 \
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-max_target_seqs 50 \
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-outfmt 5
  
 
</pre>
 
</pre>
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−
 
  
 
==Further Information==
 
==Further Information==
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* [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]
  
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{|
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{{Modulepagenav}}
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|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
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|style="width:95%; border-width: 0" |
 
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* [[Main_Page|Home]]
 
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* [[Applications|Application support]]
 
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* [[General|General]]
 
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* [[Training|Training]]
 
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* [[Programming|Programming support]]
 
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|-
 
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|}
 

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

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