On Aug 21, 2014, at 09:18 , Nils Homer <nho...@broadinstitute.org> wrote: > This is certainly a strange issue. Perhaps there is a problem using the > intel deflator with your JVM and environment. Could you retry by adding to > your java command "-Dtry_use_intel_deflater=false"? You could also move the > "libIntelDeflater.so" away from the path. You should see a difference in the > version line that the tool outputs to stderr: > > amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01; Picard version: > 1.118(2329276ea55d31ab6b19bab55b9ee7b51e4a446e_1406559781) IntelDeflater > > The IntelDeflator should say JdkDeflator if you turned that feature off > properly.
I've disabled it and after a few runs still see a JVM crash. I don't know if it's an accurate measure of what's happening in Java space, but allowing `strace -c -p …` to gather stats on the MarkDuplicates thread for a while reports nearly 100% of time in futex(). The runtime is still dramatically different from my other input, and I wonder if you have any ideas why? Do you expect it's some property of the data? Or some pathological edge case? I can't help but think the crash and runtime leap are related... ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
