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segment fault of picard MarkDuplicates when RNA-seq BAM

See original GitHub issue

segment fault of picard MarkDuplicates when RNA-seq BAM.

Bug Report

Affected tool(s)

MarkDuplicates

Affected version(s)

2.14.1/Latest 2.15.0
but 2.10.3. is OK

Description

segment fault of picard MarkDuplicates when RNA-seq BAM. although we do not use the bam without dup any more, but we can see how many dup in it.

Steps to reproduce

[Tue Nov 14 10:52:58 CST 2017] MarkDuplicates INPUT=[/biowrk/refseq.Homo_sapiens.108/bam.star/SAMEA1968189/Aligned.sortedByCoord.out.bam] OUTPUT=/biowrk/refseq.Homo_sapiens.108/bam.star/SAMEA1968189/md.bam METRICS_FILE=/biowrk/refseq.Homo_sapiens.108/bam.star/SAMEA1968189/md.metrics REMOVE_DUPLICATES=true VERBOSITY=WARNING COMPRESSION_LEVEL=0 CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Nov 14 10:52:58 CST 2017] Executing as root@T620 on Linux 3.10.0-693.5.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_151-b12; Deflater: Intel; Inflater: Intel; Picard version: 2.15.0-SNAPSHOT
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f8b2a6da58b, pid=29322, tid=0x00007f830d745700
#
# JRE version: OpenJDK Runtime Environment (8.0_151-b12) (build 1.8.0_151-b12)
# Java VM: OpenJDK 64-Bit Server VM (25.151-b12 mixed mode linux-amd64 )
# Problematic frame:
# V  [libjvm.so+0x62e58b]
#
# Core dump written. Default location: /usr/hpc-bio/bam.align/core or core.29322
#
# An error report file with more information is saved as:
# /usr/hpc-bio/bam.align/hs_err_pid29322.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#

Issue Analytics

State:
Created 6 years ago
Comments:6 (1 by maintainers)

Top GitHub Comments

1reaction

wangyuguicommented, Nov 15, 2017

@lbergelson

use_jdk_deflater=true use_jdk_inflater=true => OK use_jdk_deflater=true =>OK use_jdk_inflater=true =>segment fault too.

0reactions

wangyuguicommented, Dec 10, 2017

In my test, it is fixed in picard 2.16.0 release.

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