Re: [Useq-users] ChIPSeq java error

[David N. <dav...@gm...>]

OK Andrew,  the latest release 8.1.6 fixes your java issue with the RNASeq
and ChIPSeq apps.  -cheers, D

From:  Nicholas Dickens <Nic...@gl...>
Date:  Tue, 7 Feb 2012 08:26:00 -0000
To:  "Oler, Andrew (NIH/NIAID) [C]" <and...@ni...>, David Nix
<dav...@hc...>
Cc:  <use...@li...>
Subject:  Re: [Useq-users] ChIPSeq java error

RE: [Useq-users] ChIPSeq java error
Can you edit your path (depending on your shell either export PATH= in bash
or set PATH for tcsh) and reset it completely so it doesn't look in /usr/bin
... temporarily resetting it while you are using Useq.

Best wishes,

Nick

Nick  Dickens
DPhil BSc ARCS
Genome and Data Analyst

Wellcome Trust Centre for Molecular Parasitology
B6-21 Glasgow Biomedical Research Centre
120 University Place
Glasgow G12 8TA, UK
Tel: +44 (0)141 330 8282



-----Original Message-----
From: Oler, Andrew (NIH/NIAID) [C] [mailto:and...@ni...]
Sent: Mon 2012-02-06 19:37
To: David Nix
Cc: use...@li...
Subject: [Useq-users] ChIPSeq java error

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
Bethesda, MD 20892
Mobile: 240-507-3791
Office: 301-402-5685
http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/>
(Within NIH)
http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public)

Disclaimer: The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be used by
anyone who is not the original intended recipient. If you have received this
e-mail in error please inform the sender and delete it from your mailbox or
any other storage devices. National Institute of Allergy and Infectious
Diseases shall not accept liability for any statements made that are
sender's own and not expressly made on behalf of the NIAID by one of its
representatives.


----------------------------------------------------------------------------
--
Try before you buy = See our experts in action!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-dev2
_______________________________________________
Useq-users mailing list
Use...@li...
https://lists.sourceforge.net/lists/listinfo/useq-users

----------------------------------------------------------------------------
-- Keep Your Developer Skills Current with LearnDevNow! The most
comprehensive online learning library for Microsoft developers is just
$99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style
Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-d2d_________________________________________
______ Useq-users mailing list Use...@li...
https://lists.sourceforge.net/lists/listinfo/useq-users