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sivarajankumar / fluxcapacitor

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Error appending data to profile on windows #59

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
For which program(s) you want a new feature?
(Capacitor/Simulator/Both/Tetris)
Simulator

Which build of the program(s)?
(look it up in the .prop file in the ./bin folder of the installation)
RC2

What operating system you use?
(unix32, unix64, win32, win64, macPPC32, macX8632, macX8664, other;
see /proc/cpuinfo, Settings->Control Panel->System, Apple->About this Mac)
Windows

Starting RC2 on a windows box with the yeast demo data gives an error while 
appending data to the initial profile:

C:\Users\Invitado\Desktop\fluxsimulator_demo_yeast>flux -t simulator -p 
yeast_demo.par -x
[INFO] I am the Flux Simulator ( Devel Mode ), nice to meet you!

[INFO] I am collecting information on the run.
        initializing profiler  ********** ERROR
[ERROR] Error while loading stats: Field 3 not found
java.lang.IllegalArgumentException: Field 3 not found
        at fbi.commons.ByteArrayCharSequence.getTokenInt(ByteArrayCharSequence.java:339)
        at fbi.genome.sequencing.rnaseq.simulation.Profiler.initializeProfiler(Profiler.java:546)
        at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:275)
        at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:32)
        at fbi.commons.flux.Flux.main(Flux.java:170)
[CAUTION] I overwrite the expression values in file yeast_demo.pro, please 
confirm:
        (Yes,No,Don't know) y

[INFO] Checking GTF file
        checking ********** OK (00:00:00)
[PROFILING] I am assigning the expression profile
        checking ********** OK (00:00:00)
        Reading reference annotation ********** OK (00:00:00)
        found 6689 transcripts

[PROFILING] Parameters
        NB_MOLECULES    500000
        EXPRESSION_K    -0.6
        EXPRESSION_X0   5.0E7
        EXPRESSION_X1   9500.0
        PRO_FILE_NAME   C:\Users\Invitado\Desktop\fluxsimulator_demo_yeast\yeast_demo.pro

        profiling ********** OK (00:00:00)
        Updating .pro file  **********[WARN] Unable to remove original .pro file, I try the move anyways
 Error
[ERROR] Error while updating .pro file: Unable to move new .pro file to its 
location!
java.lang.RuntimeException: Unable to move new .pro file to its location!
        at fbi.genome.sequencing.rnaseq.simulation.ProfilerFile.appendProfile(ProfilerFile.java:146)
        at fbi.genome.sequencing.rnaseq.simulation.Profiler.profile(Profiler.java:357)
        at fbi.genome.sequencing.rnaseq.simulation.Profiler.call(Profiler.java:124)
        at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:319)
        at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:32)
        at fbi.commons.flux.Flux.main(Flux.java:170)
 FAILED
[ERROR] Error while profiling :Unable to append data to profile file!
java.lang.RuntimeException: Error while profiling :Unable to append data to 
profile file!
        at fbi.genome.sequencing.rnaseq.simulation.Profiler.profile(Profiler.java:363)
        at fbi.genome.sequencing.rnaseq.simulation.Profiler.call(Profiler.java:124)
        at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:319)
        at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:32)
        at fbi.commons.flux.Flux.main(Flux.java:170)
Caused by: java.lang.RuntimeException: Unable to append data to profile file!
        at fbi.genome.sequencing.rnaseq.simulation.Profiler.profile(Profiler.java:358)
        ... 4 more

Original issue reported on code.google.com by thasso.g...@gmail.com on 7 Jul 2011 at 5:09

GoogleCodeExporter commented 8 years ago 
tested demo dataset on WindowsXP (32bit) and Windows 7 (32bit). Put the demo 
dataset in the same folder (default Desktop), tested both, complete run and 
command line reported to be problematic (-x). No error has been produced.

Original comment by gmicha@gmail.com on 2 Sep 2011 at 3:19

GoogleCodeExporter commented 8 years ago 
Closed after not being able to reconstruct on different windows boxes. Possibly 
aberrant behavior was removed by Windows-specific patches included in 
fbi.genome.simulator-1.0-RC4.tar.gz

Original comment by gmicha@gmail.com on 5 Sep 2011 at 12:46