PBS Tutorial BLAST

Scenario: You have a fasta file, called my_seqs.fasta, with multiple nucleotide sequences in it that you would like to compare to NCBI's nr using Charlie.

What do you do?

Getting on Charlie:

1. On your local machine, move your fasta file into a directory system that you have access to on Charlie.

2. Open up a terminal, sign into the charlie front end ssh [email protected]

3. Navigate into the directory that contains your fasta file cd /mounted/fs/blasts/
   3a. Check to see that your fasta file is in the directory you've navigated to: ls my_seqs.fasta

Setting up your BLAST

4. Set up your BLAST submission:

Putting together a job submission requires you provide the parameters required to submit a job, and the actual commands you will run. Job submission instructions begin with #PBS, shell commands go after the PBS parameters. So for our BLAST example, save the following, with adjusted commands and parameters for your specific BLAST, as a text file on Charlie (for example, save it as: blast_script.sh to your home directory):

#!/bin/bash

#PBS -N script-name
#PBS -V

#PBS -q route
#PBS -l walltime=00:05:00
#PBS -lselect=1:ncpus=1

#PBS -e /home/kguay/errors/
#PBS -o /home/kguay/out/
  
module use /mod/scgc
module load blast
blastx -query my_seqs.fasta -db nr -outfmt 6 -num_descriptions 10 -num_alignments 10 -evalue 0.001 -num_threads 8 -o outputblastfile.txt

Submit the job

Once you've put together this submission text, submit the job by typing:
qsub ~/blast_script.sh

You can see the status of your submitted job (and all jobs in the queue) by typing: qstat -a

Once your job is finished, it will disappear from the queue.

What does it all mean?

PBS commands breakdown

Script name will show up in the PBS queue:
#PBS -N script-name

Use submission environment:
#PBS -V

Choose which queue to submit to:
link here to PBS queues options
#PBS -q route

Set max time for run:
#PBS -l walltime=00:20:00

TODO: My understanding of this particular command is fuzzy. For BLAST, there's a --num_threads command. If I input num_threads=20 then should my ncpus=20? Leave select=1 regardless of how many cpus you are using. Set the number of nodes and cpus per node:
#PBS -l select=1:ncpus=1

Sends error outputs to specific directory
#PBS -e /home/kguay/errors/

Sends standard outputs to specific directory
#PBS -o /home/kguay/out/

BLAST command breakdown

1. Load the required module system
   For SCGC's packages, you would use the command:
   module use /mod/scgc

2. Load the required programs, in this case, we just need SCGC's default BLAST:
   module load blast

3. Run BLAST, An example command:

blastx -query [input fasta name] -db nr -outfmt 6 -num_descriptions 10 -num_alignments 10 -evalue 0.001 -num_threads 8 -out outputblastfile.txt

BLAST output options