Sequencing fails with JVM crash related to ZIP file

Starting
Writing parameter file
Parameters written:
NB_MOLECULES  250000000
READ_NUMBER 100000000
#NB_MOLECULES  250000
#READ_NUMBER 100000
READ_LENGTH 76
ERR_FILE 76
PAIRED_END  true
FASTA   true


FRAGMENTATION   true
FRAG_SUBSTRATE  RNA
#FRAG_EZ_MOTIF
FRAG_METHOD UR

PCR_DISTRIBUTION    default

FILTERING   YES
SIZE_SAMPLING   MH
SIZE_DISTRIBUTION /home/devel/thasso/data/simulator_insert_size_dist.isizes

RTRANSCRIPTION  true
#RT_MOTIF
RT_PRIMER   RH
RT_LOSSLESS true
REF_FILE_NAME _uncompressed_13235_dm3_flyBaseGene_fromUCSC111123.gtf
GEN_DIR /scratch/devel/thasso/data/jip/data/genomes/dm3
PRO_FILE_NAME /scratch/devel/thasso/data/jip/runs/SO-sim3_212/profiler/SO-Simulation.pro
LIB_FILE_NAME /scratch/devel/thasso/data/jip/runs/SO-sim3_212/lib/lib_split_7/SO-Simulation-8.lib
SEQ_FILE_NAME SO-Simulation-8.bed
TMP_DIR /scratch/devel/thasso/data/jip/runs/SO-sim3_212/sequencer/sequencer_split_7/tmpdir
Starting simulator
[INFO] I am the Flux Toolbox (v1.0-SNAPSHOT build 1096), nice to meet you!

[INFO] I am collecting information on the run.
        initializing profiler  [DEBUG] Counted 21223 in /scratch/devel/thasso/data/jip/runs/SO-sim3_212/profiler/SO-Simulation.pro
**********

[INFO] Loading Fragmentation from /scratch/devel/thasso/data/jip/runs/SO-sim3_212/lib/lib_split_7/SO-Simulation-8.lib
[INFO] Reading error model 76 bases model

[INFO] Checking GTF file
*[WARN] Unsorted in line 667 - chr/strand chr4 + already read.
[GTF FILE] The GTF reference file given is not sorted, sorting it right now...
        sorting GTF file  OK (00:00:24)
[GTF FILE] The Simulator will use /scratch/devel/thasso/data/jip/runs/SO-sim3_212/sequencer/sequencer_split_7/_uncompressed_13235_dm3_flyBaseGene_fromUCSC111123_sorted.gtf
[GTF FILE] You might want to update your parameters file
[INFO] you did not ask for expression, I skip it.

[INFO] you did not want me to construct the library, I skip it.


[SEQUENCING] getting the reads
        initialize
        zipping ********** 2141523725 lines zipped (3302655675 fragments) (03:10:45)
        sequencing #
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00002aaaaad181b0, pid=13298, tid=1092548928
#
# JRE version: 6.0_26-b03
# Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libzip.so+0xb1b0]  __int128+0x60
#
# An error report file with more information is saved as:
# /scratch/devel/thasso/data/jip/runs/SO-sim3_212/sequencer/sequencer_split_7/hs_err_pid13298.log
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
/project/devel/rna_pipeline/usr/bin/flux: line 50: 13298 Aborted                 java -Xmx$FLUX_MEM -DwrapperDir="$dir/bin" $MISC -cp $cp fbi.commons.flux.Flux "$@"

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  java.util.zip.ZipFile.getNextEntry(JI)J+0
j  java.util.zip.ZipFile.access$400(JI)J+2
j  java.util.zip.ZipFile$2.nextElement()Ljava/util/zip/ZipEntry;+54
j  java.util.zip.ZipFile$2.nextElement()Ljava/lang/Object;+1
j  fbi.genome.sequencing.rnaseq.simulation.Sequencer.sequence(Ljava/io/File;Ljava/io/File;)Z+258
j  fbi.genome.sequencing.rnaseq.simulation.Sequencer.call()Ljava/lang/Void;+83
j  fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call()Ljava/lang/Void;+605
j  fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call()Ljava/lang/Object;+1
j  fbi.commons.flux.Flux.main([Ljava/lang/String;)V+485
v  ~StubRoutines::call_stub