Hi, Could you add java 1.7 to the dependency list of the gatk 1.4 suite in the main toolshed. Moving from built-in to toolshed version (including the downloaded jars) after the last upgrade, GATK 1.4 tools crashed on : Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(Unknown Source) at java.lang.ClassLoader.defineClass(Unknown Source) at java.security.SecureClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.access$000(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) Could not find the main class: org.broadinstitute.sting.gatk.CommandLineGATK. Program will exit. adding sun-jre-7 to the PATH as first java option solved this. I thought that only gatk > 2.6 depended on java-7, so I'm not sure why this is happening. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer