Purdue University

Commands

• blastn
• blastp
• blastx
• blast_formatter
• amino-acid-composition
• between-two-genes
• blastdbcheck
• blastdbcmd
• blastdb_aliastool
• cleanup-blastdb-volumes.py
• deltablast
• dustmasker
• eaddress
• eblast
• get_species_taxids.sh
• legacy_blast.pl
• makeblastdb
• makembindex
• makeprofiledb
• psiblast
• rpsblast
• rpstblastn
• run-ncbi-converter
• segmasker
• tblastn
• tblastx
• update_blastdb.pl
• windowmasker

Module

You can load the modules by:

module load biocontainers
module load blast

BLAST Databases

Local copies of the blast dabase can be found in the directory /depot/itap/datasets/blast/latest/. The environment varialbe BLASTDB was also set as /depot/itap/datasets/blast/latest/. If users want to use cdd_delta, env_nr, env_nt, nr, nt, pataa, patnt, pdbnt, refseq_protein, refseq_rna, swissprot, or tsa_nt databases, do not need to provide the database path. Instead, just use the format like this -db nr.

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run BLAST on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=blast
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers blast

blastp -query protein.fasta -db nr -out test_out -num_threads 4