Magic-BLAST on Biowulf

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump, and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
The following sample session (user input in bold) is based on cookbooks from the official documentation:

[user@biowulf]$ sinteractive --cpus-per-task 8
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load magicblast

[user@cn3144 ~]$ makeblastdb -in my_reference.fa -out my_reference -parse_seqids -dbtype nucl 
[user@cn3144 ~]$ magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db my_reference
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load magicblast
magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db my_reference

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. magicblast.swarm). For example:

cd sample1 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference
cd sample2 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference
cd sample3 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference
cd sample4 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference

Submit this job using the swarm command.

swarm -f magicblast.swarm [-g #] -t # --module magicblast
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module magicblast Loads the Magic-BLAST module for each subjob in the swarm