BLAST+¶
BLAST+ consists of a number of command-line applications for sequence database search, filtering and comparing tools, creating blast databases and masking low complexity sequence.
BLAST+ is available as a module on Apocrita.
Usage¶
To run the default installed version of BLAST+, simply load the blast+
module:
$ module load blast+
$ blastn -h
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
...
Core usage and core limitation in a multithreaded run
- To ensure that BLAST+ uses the correct number of cores, the
-num_threads=${NSLOTS}
option should be used. - BLAST+ supports a maximum of 32 cores.
A list of all BLAST+ applications and options can be found here.
Example job¶
Serial job¶
Here is an example job for BLAST+ running on 4 cores and 4GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load blast+
blastn -num_threads ${NSLOTS} \
-out blast_serial.tsv \
-outfmt 6 \
-db nt \
-query GRCh38_chr1_1percent.fasta