Couldn't read from file
Couldn't open input file dna.dat
Out of memory
java -version
and make sure that you are running Version 1.1. If you have Version 1.2 or higher installed, JAMBE will not run properly.
dna.dat.
infile is missing.
java.lang.OutOfMemoryError
In this case the file
resultsAllTopos.out
is too big. The program SubsetSelection.java overcomes
this problem by thinning out the file
resultsAllTopos.out.
This allows carrying out the analysis on a subset
of the sampled topologies, and is also useful for a
consistency check: Repeating the analysis with different
thinning parameters should not dramatically change the results.
The two parameters used by the program are:
1) delta:
Skips every deltath topology.
2) offset:
Keeps topologies with this value in the MOD operation.
The program goes through all topologies and keeps those that satisfy the condition:
mod(i,delta)==offset
where i counts the topologies,
and mod is the remainder of an integer
division.
The values for delta and offset
are specified in the program
and have the following default parameters:
1) delta = 2
2) offset = 0
Change the Java code if you want to change them
or read them in from an external file.
The output of SubsetSelection.java
is written to standard output; so use redirection
to get it into the desired file.
Note that, by default, topologies are read in
from the file resultsAllTopos.out.
You need to change the Java code if you want to change
this.
Example:
java SubsetSelection > outputFile
This reads in the topologies from file
resultsAllTopos.out, discards every
2nd topology (if no changes to the code have been made),
and writes the results out to file
outputFile.
Now rename outputFile to
resultsAllTopos.out,
mv resultsAllTopos.out resultsAllTopos.bak
mv outputFile resultsAllTopos.out
JambeAnalyseTopos.java:
java JambeAnalyseTopos
If this still gives you an out-of-memory error, repeat
the precedure to further reduce the size of
resultsAllTopos.out.