no FASTQ file created

[GoogleCodeExporter]

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

Which build of the program(s)?
20101223

What operating system you use?
Mac OS 10.6.5

What steps will reproduce the problem?
1.annotation 
2.expression
3.library construction
4.sequencing

What is the expected output? What do you see instead?
A BED and a FASTQ file. Neither was generated.

Feel free to provide any additional information below.

The problem always occur at step 4. No matter I run the sequencing step through 
GUI or I use "./bin/sim.sh -p test.par -xls". It always broke with the message 
below. The err file I used was the downloaded from the sample data. And 
attached is my PAR file. 

[SEQUENCING] getting the reads
    PRO_FILE_NAME   /Users/z/Downloads/FluxSimulator/chr1/another/another.pro
    SEQ_FILE_NAME   /Users/z/Downloads/FluxSimulator/chr1/another/another.bed
    READ_LENGTH 36
    READ_NUMBER 50000
    initing **********
    6007970 lines submitted
    zipping **********
    6007970 lines zipped
    sequencing **********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.FluxSimulator.G(Unknown Source)
    at genome.sequencing.rnaseq.simulation.FluxSimulator.run(Unknown Source)
    at genome.sequencing.rnaseq.simulation.FluxSimulator.main(Unknown Source)
 FAILED

[END] I finished, took me 136 sec.

Original issue reported on code.google.com by zhaoha...@gmail.com on 22 Mar 2011 at 9:57

• Merged into: #48

Attachments:

• another.par

[GoogleCodeExporter]

Original comment by thasso.g...@gmail.com on 1 Apr 2011 at 5:25

• Added labels: Simulator

[GoogleCodeExporter]

Looks like the same issues as in #48.

Original comment by thasso.g...@gmail.com on 4 Apr 2011 at 9:47

• Changed state: Duplicate