ARCHIVED: Using RepeatMasker on Big Red
RepeatMasker is a program for finding and removing repeated low-complexity regions in DNA sequences. At Indiana University, RepeatMasker 3.2.6 is available on Big Red. It is configured to use the REBASE database and cross-match search engines. A list of frequently asked questions about RepeatMasker is available online.
RepeatMasker is a restricted-use package available only to CAP3 group users. If would like to use RepeatMasker on Big Red, read the academic user agreement and the registration form, and then email the UITS Scientific Applications and Performance Tuning (SciAPT) team with your request. In your message, note your agreement to the license terms, and provide the information requested in the user agreement and registration form. After SciAPT staff receive your license agreement, they will add you to the CAP3 group, and email you a confirmation notification.
After receiving your confirmation in email, you can add RepeatMasker to your user environment and begin using it:
- To add RepeatMasker temporarily, at the command prompt, enter: soft add +RepeatMasker
- To add RepeatMasker permanently, add
~/.softfile, save the file, and then enter
resoftat the command prompt.
The introduction document file is available on Big Red at:/N/soft/linux-sles9-ppc64/Repeatmasker/RepeatMasker/repeatmasker.help
To see the RepeatMasker options, enter
the command line, or see:
If your job will run for fewer than 20 minutes, run
RepeatMasker from the command line in the directory where
your input files are located.
If your job will run for longer than 20 minutes, use the
serialjob script. For more on
its manual page (
man serialjob) and ARCHIVED: On Big Red at IU, how do I use the serialjob script to submit jobs?
RepeatMasker output will be generated in the same directory as your input files.
Note: Big Red, originally commissioned in 2006, was retired from service on September 30, 2013. Its replacement, Big Red II, is a hybrid CPU/GPU Cray XE6/XK7 system capable of achieving a theoretical peak performance (Rpeak) of 1 petaFLOPS, making it one of the two fastest university-owned supercomputers in the US. For more, see Getting started on Big Red II. If you have questions or concerns about the retirement of Big Red, contact the High Performance Systems group.
Last modified on September 27, 2013.