databasing a very large tree file for trimming

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What steps will reproduce the problem?
1. java -Xmx1500m -jar phyutility.jar -tt 100 -in file1.nex -out
trimfile1.out -derb
2.
3.

What is the expected output? What do you see instead?
The error message repeats the following:
A non SQL error occured.
java.lang.NullPointerException
        at phyutility.drb.WwdEmbedded.addTree(WwdEmbedded.java:112)
        at
phyutility.jebl2jade.NexusToJade.getJadeFromJeblNexusDerby(NexusToJade.java:57)
        at phyutility.mainrunner.Main.getNewickFromNexusDerby(Main.java:1103)
        at phyutility.mainrunner.Main.thin(Main.java:935)
        at phyutility.mainrunner.Main.runArgs(Main.java:371)
        at phyutility.mainrunner.Main.<init>(Main.java:66)
        at phyutility.mainrunner.Main.main(Main.java:1509)
 . . . exception thrown:

What version of the product are you using? On what operating system?
MacOSX_Intel with Java 1.5 and am using phyutility v2.2

Please provide any additional information below.

Original issue reported on code.google.com by christen...@yale.edu on 13 Feb 2008 at 7:34

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I think I know the problem. A fix is started.

Original comment by blackrim on 28 Feb 2008 at 8:58

• Changed state: Started

[GoogleCodeExporter]

Should be fixed now. I will upload a new version of phyutility soon, but until 
then you can just replace your 
existing phyutility.jar with the one here 
http://www.blackrim.org/programs/dist/phyutility.jar.

Original comment by blackrim on 10 Mar 2008 at 9:41

• Changed state: Fixed