No fasta file produced

[GoogleCodeExporter]

For which program(s) you want a new feature?
Simulator

Which build of the program(s)?
(look it up in the .prop file in the ./bin folder of the installation)

# simulator properties

    simulator.build = 20101223
    simulator.jdk = 1.5

What operating system you use?
Mac OSX

What steps will reproduce the problem?
1. Run new project, provide gtf file with the annotation; the genomic sequence 
(.fa file) is provided in a folder which was selected as the "Genome Folder". 

2. Run Fluxsimulator with default parameters. The annotation step, the 
expression step and the library step are fine (parameters for the library step: 
fragmentation, physical shearing, cutoff with default parameter values). For 
the sequencing step: I choose the option "enable FastA / FastQ output"; I did 
not  choose "enable positional error"

3. What is the expected output? What do you see instead?

Expected output: Fasta file containing the sequences of the read.
But: Error occurs, no Fasta file is produced

Feel free to provide any additional information below.

I got the following error (sequencing step stopped): 

java.lang.ArrayIndexOutOfBoundsException
    at java.lang.System.arraycopy(Native Method)
    at genome.sequencing.rnaseq.simulation.A.A(Unknown Source)
    at genome.sequencing.rnaseq.simulation.A.A(Unknown Source)
    at genome.sequencing.rnaseq.simulation.A$_A.A(Unknown Source)
    at genome.sequencing.rnaseq.simulation.A$_A.run(Unknown Source)
    at genome.sequencing.rnaseq.simulation.A.x(Unknown Source)
    at genome.sequencing.rnaseq.simulation.A.run(Unknown Source)
    at genome.sequencing.rnaseq.simulation.A.A.run(Unknown Source)
    at java.lang.Thread.run(Thread.java:680)
    at genome.sequencing.rnaseq.simulation.A.E$_A.run(Unknown Source)

Thanks for any help!

Original issue reported on code.google.com by jkielba...@gmail.com on 22 Feb 2011 at 3:53

• Merged into: #48

[GoogleCodeExporter]

Hi,

thank you for your detailed report. If the error is reproduceable in each run, 
i.e., for each consecutive library expression and sequencing process, I would 
like to ask you to post your parameter file.

Original comment by gmicha@gmail.com on 23 Feb 2011 at 6:44

[GoogleCodeExporter]

Hi,

thank you for your fast answer! Yes, the error occured at each run. Here is the 
par file (of one specific run, I used as reference annotation the chromosome 2L 
of Drosophila):

REF_FILE_NAME   /Users/Documents/FluxSimulator/MyData/SimulatorRuns/Data/chromo2L.
gtf
PRO_FILE_NAME   /Users/Documents/FluxSimulator/MyData/SimulatorRuns/DM_chr2L_part/
TestRun/TestRun.pro
LIB_FILE_NAME   /Users/Documents/FluxSimulator/MyData/SimulatorRuns/DM_chr2L_part/
TestRun/TestRun.lib
SEQ_FILE_NAME   /Users//Documents/FluxSimulator/MyData/SimulatorRuns/DM_chr2L_part
/TestRun/TestRun.bed
GEN_DIR /Users/Documents/FluxSimulator/MyData/SimulatorRuns/Data/GenDMchr2L
TMP_DIR /var/folders/52/5269rE4ZGdCGuQVOB+lAA++++TI/-Tmp-
NB_MOLECULES    5000000
EXPRESSION_K    -0.6
EXPRESSION_X0   5.0E7
EXPRESSION_X1   9500.0
TSS_MEAN    25.0
POLYA_SHAPE 2.0
POLYA_SCALE 300.0
RT_MIN  500
RT_MAX  5500
RT_PRIMER   RANDOM
FRAGMENTATION   YES
FRAG_B4_RT  NO
FRAG_MODE   CHEMICAL
FRAG_LAMBDA 700.0
FRAG_THRESHOLD  0.1
FILTERING   YES
LOAD_CODING YES
LOAD_NONCODING  YES
FILT_MIN    200
FILT_MAX    250
READ_NUMBER 4677310
READ_LENGTH 36
PAIRED_END  NO
FASTQ   YES
QTHOLD  33.0

Original comment by jkielba...@gmail.com on 24 Feb 2011 at 12:28

[GoogleCodeExporter]

I also have this exact problem. I'm wondering if it is a problem with the 
genome folder. What should the filenames and formats of the files in this 
folder?

Original comment by jm123456...@gmail.com on 27 Feb 2011 at 9:52

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

I wrote a comment a few minutes ago but I had the marvellous idea to click 
(without my consent!) on the link ``delete this comment''.

In GEN_DIR you should have one file per chromosome. The filenames should 
correspond to the chromosome names in your GTF file (REF_FILE_NAME). The first 
column of this file contains chromosome names. For example, if you have chr2 as 
chromosome name, you must have a chr2.fa in your GEN_DIR directory.
Hope this helps.

Original comment by mikael.s...@gmail.com on 24 Mar 2011 at 3:49

[GoogleCodeExporter]

I tried, but it always produced the same error. 

There seems to be a problem with the latest version (build 20101223). I tried 
with the built 20101210 and the fasta file was produced.
Thanks for your help!

Original comment by jkielba...@gmail.com on 25 Mar 2011 at 9:00

[GoogleCodeExporter]

Original comment by thasso.g...@gmail.com on 1 Apr 2011 at 5:24

• Added labels: Simulator

[GoogleCodeExporter]

Original comment by thasso.g...@gmail.com on 4 Apr 2011 at 9:45

• Changed state: Duplicate