Wondering if anyone has reported this for the doc/sample file team: Isn't the java config example line in that file wrong (at least for my java 1.6): <env id="_JAVA_OPTIONS">-Xmx=6GB</env> With a setting of -Xmx=10g, Picard wouldn't run sortSam, instead this stderr text: ***************** Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Xmx=10g Invalid maximum heap size: -Xmx=10g Could not create the Java virtual machine. ***************** I changed the <env> tag to take out "=" so it reads: <env id="_JAVA_OPTIONS">-Xmx6G</env> and now its working fine! Had to lookup -Xmx param format on the net from: http://javahowto.blogspot.ca/2006/06/6-common-errors-in-setting-java-heap.ht... Regards, Damion. Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada