FluxSim Aborted During Sequencing Step

Summary:

command line version of FluxSimulator aborting during sequencing stage

FluxSim Aborted During Sequencing Step

W C (guest) 28 Jul 2010 23:19

Hi Micha or whomever,

I've found FluxSimulator useful, so thanks for building it.

I've been able to accomplish a few full runs, but now I'm hitting an error with the sequencing stage (I have FASTQ file generation turned on as well).

First, Here's the output from FluxSim on the Linux command line:

[HELLO] I am the Flux Simulator (build 20100526), nice to meet you!

[INIT] I am collecting information on the run.
initializing profiler *

initializing library *
Reading error model **

[NOEXPR] you did not ask for expression, I skip it.

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

[SEQUENCING] getting the reads
PRO_FILE_NAME hg19_chr10.75.pro
SEQ_FILE_NAME hg19_chr10.75.bed
READ_LENGTH 36
READ_NUMBER 500000
initing
1274015 lines submitted
zipping ****
1274015 lines zipped
sequencing **

It stops there within 20 minutes of starting (just the sequencing step).

The error it outputs is:

1. A fatal error has been detected by the Java Runtime Environment:

#

1. Internal Error (safepoint.cpp:237), pid=9505, tid=1075882304
2. Error: guarantee(PageArmed == 0,"invariant")

#

1. JRE version: 6.0_17-b04
2. Java VM: Java HotSpot(TM) 64-Bit Server VM (14.3-b01 mixed mode linux-amd64 )
3. An error report file with more information is saved as:
4. hs_err_pid9505.log

#

1. If you would like to submit a bug report, please visit:
2. http://java.sun.com/webapps/bugreport/crash.jsp

#
../../../FluxSimulator/bin/sim.sh: line 3: 9505 Aborted java -Xmx1G -XX:-UseBiasedLocking -DwrapperDir="$scriptdir" -jar "$scriptdir/../lib/FluxSimulator.jar"

I can post the log file is needed, but I didn't find it that useful.

Here's my .par file:

REF_FILE_NAME Homo_sapiens.GRCh37.58.chr10_sorted.gtf
PRO_FILE_NAME hg19_chr10.75.pro
LIB_FILE_NAME hg19_chr10.75.lib
SEQ_FILE_NAME hg19_chr10.75.bed
GEN_DIR chr10.fa
TMP_DIR /tmp
NB_MOLECULES 5000000
EXPRESSION_K -0.6
EXPRESSION_X0 5.0E7
EXPRESSION_X1 9500.0
TSS_MEAN 25.0
POLYA_SHAPE 0.0
POLYA_SCALE 0.0
RT_MIN 500
RT_MAX 5500
RT_PRIMER RANDOM
FRAGMENTATION YES
FRAG_B4_RT YES
FRAG_MODE PHYSICAL
FRAG_LAMBDA 900.0
FRAG_SIGMA 0.05
FRAG_THRESHOLD 0.1
FILTERING YES
LOAD_CODING YES
LOAD_NONCODING YES
FILT_MIN 200
FILT_MAX 250
READ_NUMBER 500000
READ_LENGTH 36
PAIRED_END YES
FASTQ YES
ERR_FILE_NAME ../FluxSimulator/demo/error_model_qualities.err

Thanks for any help,
wc

Re: FluxSim Aborted During Sequencing Step

Moritz (guest) 09 Aug 2010 14:14

Hey wc,

did you find any solution for your problem? I have a very similar error and I wondered how the "directory with genomic sequences split by chromosome" (GEN_DIR) should be organized. Should it contain simple fasta files named 1.fa 2.fa etc. (naming them chr1.fa chr2.fa etc. produced another error in my case).

Best
Moritz

Goje (guest) 10 Jun 2011 07:52

Hey guys.
I've got the same problem, except that the program stops running without reporting any errors!
This is when it stays stale:

READ_LENGTH 50
READ_NUMBER 2000000
initing

gmicha 17 Jun 2011 13:48

Hi,

seems like the symptoms reported in Issue52, please try to report problems of technical nature there. Note that we uploaded a largely redesigned simulator version (1.0 RC1), which also excludes parallelization that seemed to cause JVM/OS-dependent crashes or deadlocks. I will try to update the webpages with new documentation ASAP, for the moment please refer to the readme file bundled in the tarball. Also, additional logging depth is provided by the —log DEBUG parameter, please post a corresponding stderr output with your bug report if the problem persists for you.

cheers