FASTA programs on Big Red

On this page:

• General introduction and usage policy
• Parallel version
• Serial version
• Help documents and manual pages

General introduction and usage policy

The FASTA programs search sequence databases for sequences that are similar to a set of query sequences. Both serial and parallel versions are available on Big Red at Indiana University. If you are familiar with the FASTA package and have a large amount of data to analyze, try the parallel version.

Jobs using the parallel version are submitted to the LONG queue, which lets you request up to 128 processors for 336 hours (14 days). Also available are the NORMAL queue, which lets you request up to 1,024 processors for 48 hours (two days), and the DEBUG queue, which lets you request up to 16 processes for up to 15 minutes. For more, see the "Computational resources" section of Big Red usage policies.

Parallel version

To run parallel FASTA programs, use the fastajob shell script. The fastajob script is necessary, because programs in the FASTA package have been compiled to use multiple processes. The fastajob should be in your path by default, and its manual page should be in your path of manual pages. The syntax for fastajob is:

Replace program_to_run with the name of the FASTA program to run, program_options with command line options, n with the number of processors to use, and queue_name with the queue to which you're submitting the job. If you omit the -CPUS option, 4 processors will be used. To request more than four processors, specify an integer value that is a multiple of 4. If you specify a value that is not a multiple of 4, the value will be increased to the next multiple of 4. The maximum number of processors is 128 (unless you also specify a larger queue). If you omit the -wallhours option, your job will be allowed to run for 2 hours. Use the -wallhours option to request more time.

For example, to submit a batch job that runs tfastx to query sequences in file myseqs.aa against the FASTA-formatted database refseq.nt, use:

To run the same program with the same data using 16 processes, use:

To run the same program using up to 10 hours of wall clock time, use:

When you run fastajob, you'll receive a message when your job is submitted to the queue and another when the job finishes. To check the status of your job, use the llq command.

The FASTA package contains many programs with names that include the package version number and the parallel programming library used to build them. The fastajob script will accept either a nickname or the name of the actual binary. Nicknames for most programs are below:

Output from FASTA is stored in a file named after your job number. You can request other output files using the -O option on the command line. The fastajob script produces fastajob.99999.out and fastajob.99999.err, where 99999 is the number of your job. The .out file contains results (Unix standard output), and the .err file contains debugging output and error messages (Unix standard error). FASTA usually prints some processing information to the standard error file even though the information does not reflect errors. It writes results to the output file unless you use the -O option on the command line.

Serial version

A serial version of the FASTA package is in:

To temporarily add that directory to your path and the manual pages to your MANPATH, use:

To have them added permanently the next time you log in, use:

Help documents and manual pages

For using the parallel or serial version, documentation is available at:

The parallel version uses the MPI parallel programming interface and the PVM parallel programming library; therefore no manual pages are available. Sample datasets are available in:

For using the serial version, see the README and documentation files in:

Also for the serial version, see the manual pages in:

For more information about the availability of software on the Indiana University shared central systems, see At IU, what software is available on the research computing systems, and how may I request that software be added?

For more information about TeraGrid software, see:

• How can I find out what software is available on the TeraGrid?
• How can I see what site-specific software is installed on a TeraGrid resource?

This document was developed with support from the National Science Foundation (NSF) under Grant No. 0503697 to the University of Chicago and subcontracted to Indiana University. Additional support was provided by IU through its participation in the TeraGrid, which is supported by the NSF under Grants No. 0833618, SCI451237, SCI535258, and SCI504075. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

Also see:

• Bioinformatics support