[Useq-users] ChIPSeq java error

[Oler, A. (NIH/N. [C] <and...@ni...>]

Hi David,

I'm running the ChIPSeq application from USeq 8.0.7 and I'm getting this error:

The following problems were encountered when processing your parameter file.  Correct and restart. ->
Your java application is not >= 1.6 (type 'java -version' on the cmd line). Install the most recent java from http://www.java.com/en/download/ .
Your save results directory exits, may overwrite the files within.

When I type java -version on the command line, I get this output:
java -version
java version "1.6.0_22"
Java(TM) SE Runtime Environment (build 1.6.0_22-b04)
Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode)

The java version is fine, so I'm not sure what the problem is.  java is an alias for a locally installed version of java, which is 1.6.  Could it be that the ChIPSeq program calls '/usr/bin/java' instead of 'java'?

/usr/bin/java -version
java version "1.4.2"
gij (GNU libgcj) version 4.1.2 20080704 (Red Hat 4.1.2-46)

Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I'm running this on a system where I can't change the binaries in /usr/bin/.  Any suggestions?

Thanks,

Andrew

Andrew Oler, Ph.D.
Contractor - Lockheed Martin
High-Throughput Sequencing Bioinformatics Specialist
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62
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