diff --git a/templates/Realignment.sh.tt b/templates/Realignment.sh.tt index 468c46f..0de130b 100644 --- a/templates/Realignment.sh.tt +++ b/templates/Realignment.sh.tt @@ -9,6 +9,8 @@ cd "[% dirs.tmp %]" assert_not_empty "[% sample_bam_path %]" java -Xmx[% opt.REALIGNMENT_MASTER_MEM %]G \ + -XX:+HeapDumpOnOutOfMemoryError \ + -XX:HeapDumpPath="[% opt.OUTPUT_DIR %]" \ -Djava.io.tmpdir="[% dirs.tmp %]" \ -jar "[% opt.GATK_QUEUE_PATH %]/Queue.jar" \ -jobQueue [% opt.REALIGNMENT_QUEUE %] \