Hi, I'm running into problems using Picard's MarkDuplicates utility. Sometimes I get a JVM crash, sometimes the process just seems to hang. After the initial startup, strace shows nothing but sched_yield() and futex() calls. While the input data which hangs has ~900k reads, MarkDuplicates runs in about 1min on ~400k reads from a different input file.
Example informational output from both crashing and hanging runs are attached, as well as the crash log of the JVM. $ java -version java version "1.7.0_67" Java(TM) SE Runtime Environment (build 1.7.0_67-b01) Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode) Any ideas? Thanks, Thomas
jvm-crash.log
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MarkDuplicates-crash.log
Description: Binary data
MarkDuplicates-hang.log
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