Difference between revisions of "Applications/Ncbi-blast"
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==Usage Examples== | ==Usage Examples== | ||
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===Command Set=== | ===Command Set=== | ||
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* update_blastdb.pl | * update_blastdb.pl | ||
* windowmasker | * windowmasker | ||
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===SLURM Script=== | ===SLURM Script=== | ||
Revision as of 13:25, 5 April 2017
Contents
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
- Modules: ncbi-blast/2.4.0
- 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
SLURM Script
#!/bin/bash
fasta=/home/user1/maker.all.proteins.fasta
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 --ntasks-per-node $threads_per_job
#SBATCH -o job-%j.out
#SBATCH -e job-%j.out
#SBATCH -p compute
#LOAD MODULE
module load ncbi-blast/2.4.0
#
date
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
echo -e \"\\\nDONE\\\n\"
date" > run_blastn_${p}.slurm.sh
sbatch run_blastn_${p}.slurm.sh
done
cd ..
done
Further Information
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