Biology Reference
In-Depth Information
make sure that the output folder contains enough free space for
the analysis. A general rule of thumb is to provide one to two
orders of magnitude more free space in the output folder
than the size of the input file. If an analysis uses up available
disk space, retry the analysis on a computer with more available
disk space.
6. While SAT´ was designed with scalability in mind, SAT´ analyses
of extremely large datasets (for example, datasets with 100,000
sequences or more) may overburden some desktop computers.
If your computational resources are exceeded and your
computer becomes unresponsive, first try to click the “Stop”
button while the analysis is running. WARNING: the following
two steps may lead to data loss, and should only be used as a last
resort. If the situation still is not resolved, next try to quit the
SAT
´
application by either clicking the close button on the
SAT´ application window or pressing COMMAND-Q. As a
last resort if the previous steps did not work, force-quit the
SAT´ application by pressing COMMAND-OPTION-ESC,
choosing the SAT´ application, and pushing the “Force Quit”
button. For more details about force-quitting an application,
7. If an analysis was canceled due to memory or time limitations,
retry the analysis under one or more of the following conditions.
Increase the “Max. Memory (MB)” setting in the “Jobs Set-
tings” window up to 90 % of physical memory. Use a computer
with a more powerful CPU and/or additional physical memory.
8. Always backup data and analysis files frequently. We suggest
using the Time Machine feature in Mac OS X to schedule
regular and frequent backups. Revert to backup files in the
event of accidental modification to or loss of files.
9. For more powerful archival and other capabilities, use a version
control system to manage storage for computational analyses
and experiments. We particularly recommend Git (
http://git-
scm.com/
).
10. In the event of installation issues, first try to update your system
using the “Software Update” feature in Mac OS X and retry the
installation.
11. Make sure that the new installation folder for the SAT´ appli-
cation is not contained within the downloaded package. The
SAT´ application will not run correctly within the downloaded
package and must be installed to a separate location.
12. Make sure that your input file is compatible with your operating
system. This situation can arise if your input file was created on a
computer running a different operating system than the
operating system on the computer running the SAT´ applica-
tion. Incompatibility can prevent the SAT
´
application from
