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):
With a setting of -Xmx=10g, Picard wouldn't run sortSam, instead this stderr
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:
and now its working fine! Had to lookup -Xmx param format on the net from:
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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