Picard MarkDuplicates fatal error
Entering edit mode
5.0 years ago
fwuffy ▴ 100

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

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

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
 - 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
 - klass: {type array byte}
 - length: 0
RDI=0x0000000000000001 is an unknown value
R8 =0x00007f7c21839b20: <offset 0x1043b20=""> in /usr/lib/jvm/java-1.8.0-openjdk- 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
 - 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.


Picard markduplicates • 2.5k views
Entering edit mode
5.0 years ago
h.mon 34k

Apparently, yes, several people had run into this before. 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.

Entering edit mode

Using 1.119 Yes Googled but ran into a different error, but this looks like it. Thanks, I will try the upgrade.

Entering edit mode

Updating to 2.17 fixed it Thanks!


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