Thursday Exercise 1.1: Understanding Data Requirements

This exercise's goal is to learn to think critically about an application's data needs, especially before submitting a large batch of jobs or using tools for delivering large data to jobs. In this exercise we will attempt to understand the input and output of the bioinformatics application BLAST, which you used in Tuesday's exercise 3.3.

Setup

  1. Log in to training.osgconnect.net
  2. Navigate to your local scratch directory:

    [email protected] $ cd /local-scratch2/<USERNAME>
    

    Replacing <USERNAME> with your username

  3. Create a directory for this exercise named thur-blast-data and change into it

Copy the Input Files

To run BLAST, we need the executable, input file, and reference database. For this example, we'll use the "pdbaa" database, which contains sequences for the protein structure from the Protein Data Bank. For our input file, we'll use an abbreviated fasta file with mouse genome information.

  1. Copy the BLAST executables:

    [email protected] $ wget http://proxy.chtc.wisc.edu/SQUID/osgschool19/ncbi-blast-2.7.1+-x64-linux.tar.gz
    [email protected] $ tar -xzvf ncbi-blast-2.7.1+-x64-linux.tar.gz
    
  2. Download these files to your current directory:

    [email protected] $ wget http://proxy.chtc.wisc.edu/SQUID/osgschool19/pdbaa.tar.gz
    [email protected] $ wget http://proxy.chtc.wisc.edu/SQUID/osgschool19/mouse.fa
    
  3. Untar the pdbaa database:

    [email protected] $ tar -xzvf pdbaa.tar.gz
    

Understanding BLAST

Remember that blastx is executed in a command like the following:

[email protected] $ ./blastx -db <DATABASE ROOTNAME> -query <INPUT FILE> -out <RESULTS FILE>

In the above, the <INPUT FILE> is the name of a file containing a number of genetic sequences (e.g. mouse.fa), and the database that these are compared against is made up of several files that begin with the same <DATABASE ROOTNAME>, (e.g. pdbaa). The output from this analysis will be printed to <RESULTS FILE> that is also indicated in the command.

Calculating Data Needs

Using the files that you prepared in thur-blast-data, we will calculate how much disk space is needed if we were to run a hypothetical BLAST job with a wrapper script, where the job:

If this sounds familiar to you, it's because we did just this in in Tuesdays's exercise 3.3! Here are some commands that will be useful for calculating your job's storage needs:

Input requirements

Total up the amount of data in all of the files necessary to run the blastx wrapper job, including the executable itself. Write down this number. Also take note of how much total data is in the pdbaa directory.

Compressed Files

Remember, blastx reads the un-compressed pdbaa files.

Output requirements

The output that we care about from blastx is saved in the file whose name is indicated after the -out argument to blastx. If you completed Tuesday's exercise 3.3, what is the size of that output file? Also, remember that HTCondor also creates the error, output, and log files, which you'll need to add up, too. Are there any other files? Total all of these together, as well.

Talk about this as a group!

Once you have completed the above tasks, we'll talk about the totals as a group.

Answers

Up next!

Next you will create a HTCondor submit script to transfer the Blast input files in order to run Blast on a worker nodes. Next Exercise