Having trouble running your analysis?
- Your files need to have UNIX line breaks. Even
if you think you have done this, check again! You can do
this with a text editor such as TextWrangeler.
- Many of the programs on the cluster (MrBayes, PAUP)
are a bit finicky about the files they accept as input. A
few file formatting tips are provided below.
- Use only alphanumeric characters in your taxon
names. DO NOT use spaces or dashes. An underscore can
be substituted for a space or dash.
- MrBayes will only recognize a subset of the
characters that PAUP recognizes. See page 10 of the
- Be sure that you designate any special characters
in the Nexus datablock (e.g., "missingdata=?",
- It is not uncommon for a node on the cluster to
malfunction. When this happens it is often an entire
computer that malfunctions and two processors are
affected. If your jobs are failing in multiples of two,
check to see if these jobs are using the same computer.
If so, it could be the computer that is causing your
- Do not use spaces in your file and directory
- Linux is case sensitive. When the instuctions specify
that a file or directory have a certain name, make sure
that you type the name exactly as given.
- Does your MrBayes input file have a ".nexus"
- When running multiple PAUP, MrBayes, Modeltest,
MrModeltest, and PAML analyses, run each one from its own
folder. This does not apply to the individual replicates
of PAUP bootstrap analyses.
- Occasionally a program will not run on the cluster
due software issues on the cluster. If you think this is
occurring, send an email to the cluster managaer Kelly
Crone Willis (firstname.lastname@example.org). Be sure to
include the name of the program you were using and the
.out and .err files that were produced.