Question: Hi, I'm running Picard MarkDuplicates on a sorted mapped BAM file. It's mapped with bwa mem, sorted with samtools sort. Pretty standard.

I'm running it from a cron job. The process seems to run almost to completion and generates a bam slightly larger than the input.

This is genomic data, an exome. Resulting BAM is around 9gb.

Maybe someone has run into this before?

Here is the command:

java -Xmx64g -Djava.io.tmpdir=/scratch -jar /usr/local/bin/picard/picard.jar MarkDuplicates I=/runFolder/mapped-sorted.bam O=/runFolder/mapped-sorted-mkdup.bam M=/runFolder/mapped-sorted-mkdup-metrics.txt

It barfs as follows near the end:

#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f7c20e53d9a, pid=15706, tid=0x00007f7c1ef1a700
#
# JRE version: OpenJDK Runtime Environment (8.0_161-b14) (build 1.8.0_161-b14)
# Java VM: OpenJDK 64-Bit Server VM (25.161-b14 mixed mode linux-amd64 )
# Problematic frame:
# V [libjvm.so+0x65dd9a]
#
# Core dump written. Default location: /var/runs/2018-03-16_11-44-13_GM1__c3hSaWxIQm/core or core.15706
#
# If you would like to submit a bug report, please visit:
# http://bugreport.java.com/bugreport/crash.jsp
#

--------------- T H R E A D ---------------

Current thread (0x00007f7c18020b90): GCTaskThread [stack: 0x00007f7c1ee1b000,0x00007f7c1ef1b000] [id=15710]

siginfo: si_signo: 11 (SIGSEGV), si_code: 128 (SI_KERNEL), si_addr: 0x0000000000000000

Registers:
RAX=0x00007f6b44000000, RBX=0x00007f6f978607b0, RCX=0x0000000000000000, RDX=0x007fffffc9fb8000
RSP=0x00007f7c1ef19bd0, RBP=0x00007f7c1ef19c20, RSI=0x00007f6f978607d0, RDI=0x0000000000000001
R8 =0x00007f7c21839b20, R9 =0x00000000000071d0, R10=0x00007f7c1dd0e000, R11=0x00007f6b523a1818
R12=0x00007f7c180f5f80, R13=0x00007f6f978607b8, R14=0x00007f6b3b7d0f68, R15=0x00007f0000000000
RIP=0x00007f7c20e53d9a, EFLAGS=0x0000000000010206, CSGSFS=0x002b000000000033, ERR=0x0000000000000000
TRAPNO=0x000000000000000d

Top of Stack: (sp=0x00007f7c1ef19bd0)
0x00007f7c1ef19bd0: 00007f6f97860750 00007f6b3b7d0f70
0x00007f7c1ef19be0: 00007f7c21839b20 0000000000000003
0x00007f7c1ef19bf0: 00007f7c21835dcc 00007f7c180f5f80
0x00007f7c1ef19c00: 00007f7c21835dcc 00007f7c180596e0
0x00007f7c1ef19c10: 00007f7c18020e00 00007f7c18020e50
0x00007f7c1ef19c20: 00007f7c1ef19d00 00007f7c21178ccf
0x00007f7c1ef19c30: 00007f7c1ef19ca0 0000000000000007
0x00007f7c1ef19c40: 00007f7c180f5f90 00007f7c21182367
0x00007f7c1ef19c50: 00007f7c2226069f 00007f6c09005190
0x00007f7c1ef19c60: 000014f26074bcef 00007f6f97860750
0x00007f7c1ef19c70: 000053fa0000d29c 00007f7c18021a50
0x00007f7c1ef19c80: 000053fb0000d29c 0000000000000c00
0x00007f7c1ef19c90: 0000000000000000 0000000000000000
0x00007f7c1ef19ca0: 00007f7c180b1100 00007f7c18008df0
0x00007f7c1ef19cb0: 00007f7c1ef19c01 871ebd8d0fe36a01
0x00007f7c1ef19cc0: 00007f7c18021a28 871ebd8d0fe36a00
0x00007f7c1ef19cd0: 00007f7c180593b0 00007f7c1ef19d40
0x00007f7c1ef19ce0: 00007f7c18020e40 00007f7c180596e0
0x00007f7c1ef19cf0: 00007f7c18020e00 00007f7c18020e50
0x00007f7c1ef19d00: 00007f7c1ef19df0 00007f7c2115a924
0x00007f7c1ef19d10: 00007f7c1ef19d60 00000000000003d8
0x00007f7c1ef19d20: 00007f7c180f5f80 00007f7c2176ce48
0x00007f7c1ef19d30: 00000002180f5f80 00007f7c18021228
0x00007f7c1ef19d40: 00007f7c2176faa0 0000000118020b00
0x00007f7c1ef19d50: 00007f7c180f5f80 00007f7c18030f78
0x00007f7c1ef19d60: 00007f7c2176ced8 00007f7c18030f00
0x00007f7c1ef19d70: 00007f7c1ef19d40 00007f7c18030f00
0x00007f7c1ef19d80: 00007f7c2176ce60 00007f7c18059300
0x00007f7c1ef19d90: 00007f7c1ef19d40 00007f7c2176ce48
0x00007f7c1ef19da0: 00007f7c1801de00 00007f7c1ef19d40
0x00007f7c1ef19db0: 00007f7c1ef19d01 871ebd8d0fe36a00
0x00007f7c1ef19dc0: 00007f7c1ef19df0 0000000000000001

Instructions: (pc=0x00007f7c20e53d9a)
0x00007f7c20e53d7a: 48 89 c8 8b 0a 48 c1 e8 03 48 d3 e8 48 89 c1 48
0x00007f7c20e53d8a: 89 c2 49 8b 40 30 83 e1 3f 48 c1 ea 06 48 d3 e7
0x00007f7c20e53d9a: 48 85 3c d0 75 b0 48 8d 05 02 c4 9d 00 80 38 00
0x00007f7c20e53daa: 0f 85 a0 00 00 00 49 8b 77 08 4c 89 ff 4c 89 45

Register to memory mapping:

RAX=0x00007f6b44000000 is an unknown value
RBX=0x00007f6f978607b0 is pointing into object: 0x00007f6f97860750
com.intel.gkl.compression.IntelDeflater
- klass: 'com/intel/gkl/compression/IntelDeflater'
RCX=0x0000000000000000 is an unknown value
RDX=0x007fffffc9fb8000 is an unknown value
RSP=0x00007f7c1ef19bd0 is an unknown value
RBP=0x00007f7c1ef19c20 is an unknown value
RSI=0x00007f6f978607d0 is an oop
[B
- klass: {type array byte}
- length: 0
RDI=0x0000000000000001 is an unknown value
R8 =0x00007f7c21839b20: in /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-0.b14.fc26.x86_64/jre/lib/amd64/server/libjvm.so at 0x00007f7c207f6000
R9 =0x00000000000071d0 is an unknown value
R10=0x00007f7c1dd0e000 is an unknown value
R11=0x00007f6b523a1818 is an unknown value
R12=0x00007f7c180f5f80 is an unknown value
R13=0x00007f6f978607b8 is an oop
java.util.zip.ZStreamRef
- klass: 'java/util/zip/ZStreamRef'
R14=0x00007f6b3b7d0f68 is pointing into metadata
R15=0x00007f0000000000 is an unknown value

Stack: [0x00007f7c1ee1b000,0x00007f7c1ef1b000], sp=0x00007f7c1ef19bd0, free space=1018k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [libjvm.so+0x65dd9a]
V [libjvm.so+0x982ccf]
V [libjvm.so+0x964924]
V [libjvm.so+0x5ddee6]
V [libjvm.so+0x91c392]

---- snipped for brevity ----

I can post the entire core dump as a file somewhere if this doesn't ring a bell.

Thanks

Answer: Apparently, yes, [several people had run into this before][1]. Solution is either 1) use Picard 2.16.0 onwards (which version are you using, by the way?), or 2) `use_jdk_deflater=true` and `use_jdk_inflater=true`.

By the way, if you did `google your own title`™, you would find that github issue between the very few first hits.

[1]: https://github.com/broadinstitute/picard/issues/975